Variants of vascular endothelial cell growth factor, their uses, and processes for their production

ABSTRACT

The present invention involves the preparation of vascular endothelial growth factor (VEGF) variants which provide materials that are selective in respect of binding characteristics to the kinase domain region and the FMS-like tyrosine-kinase region, respectively KDR and FLT-1. The respective KDR and FLT-1 receptors are bound by corresponding domains within the VEGF compound domains. The variants hereof define those two binding regions and modify them so as to introduce changes that interrupt the binding to the respective domain. In this fashion the final biological characteristics of the VEGF molecule are selectively modified.

CROSS-REFERENCE TO RELATED APPLICATIONS

This is a continuation of (provisional) patent application Ser. No.60/002,827 filed 25 Aug. 1995, for which priority benefit is herebyclaimed.

This application contains subject matter related to patent applicationU.S. Ser. No. 389,722, filed 4 Aug. 1989 (Attorney Docket 586P2) nowU.S. Pat. No. 5,332,671 and to its parent applications, U.S. Ser. Nos.369,424 filed 21 Jun. 1989 and 351,117 filed 12 May 1989.

FIELD OF THE INVENTION

The present invention is directed to particular variants of vascularendothelial cell growth factor (hereinafter sometimes referred to asVEGF), to methods for preparing such variants, and to methods andcompositions and assays utilizing such variants for producingpharmaceutically active materials having therapeutic and pharmacologicproperties that differ from the parent compound, VEGF. In particular,the assays using such variants can be employed to discover new materialshaving agonistic or antagonistic properties to VEGF.

BACKGROUND OF THE INVENTION

VEGF is a naturally occurring compound that is produced in follicular orfolliculo-stellate cells (FC), a morphologically well characterizedpopulation of granular cells. The FC are stellate cells that sendcytoplasmic processes between secretory cells.

Several years ago a heparin-binding endothelial cell-growth factorcalled vascular endothelial growth factor (VEGF) was identified andpurified from media conditioned by bovine pituitary follicular orfolliculo-stellate cells. See Ferrara et al., Biophys. Res. Comm. 161,851 (1989).

Although a vascular endothelial cell growth factor could be isolated andpurified from natural sources for subsequent therapeutic use, therelatively low concentrations of the protein in FC and the high cost,both in terms of effort and expense, of recovering VEGF provedcommercially unavailing. Accordingly, further efforts were undertaken toclone and express VEGF via recombinant DNA techniques. The embodimentsof that research are set forth in the patent applications referred tosupra; this research was also reported in the scientific literature inLaboratory Investigation 72, 615 (1995), and the references citedtherein.

In those applications there is described an isolated nucleic acidsequence comprising a sequence that encodes a vascular endothelial cellgrowth factor having a molecular weight of about 45,000 daltons undernon-reducing conditions and about 23,000 under reducing conditions asmeasured by SDS-PAGE. Both the DNA and amino acid sequences are setforth in figures forming a part of the present application—see infra.

VEGF prepared as described in the patent applications cited supra, isuseful for treating conditions in which a selected action on thevascular endothelial cells, in the absence of excessive tissue growth,is important, for example, diabetic ulcers and vascular injuriesresulting from trauma such as subcutaneous wounds. Being a vascular(artery and venus) endothelial cell growth factor, VEGF restores cellsthat are damaged, a process referred to as vasculogenesis, andstimulates the formulation of new vessels, a process referred to asangiogenesis.

VEGF is expressed in a variety of tissues as multiple homodimeric forms(121, 165, 189 and 206 amino acids per monomer) resulting fromalternative RNA splicing. VEGF₁₂₁ is a soluble mitogen that does notbind heparin; the longer forms of VEGF bind heparin with progressivelyhigher affinity. The heparin-binding forms of VEGF can be cleaved in thecarboxy terminus by plasmin to release (a) diffusible form(s) of VEGF.Amino acid sequencing of the carboxy terminal peptide identified afterplasmin cleavage is Arg₁₁₀-Ala₁₁₁. Amino terminal “core” protein, VEGF(1-110) isolated as a homodimer, binds neutralizing monoclonalantibodies (4.6.1 and 2E3) and soluble forms of FLT-1, KDR and FLKreceptors with similar affinity compared to the intact VEGF₁₆₅homodimer.

As noted, VEGF contains two domains that are responsible respectivelyfor binding to the KDR (kinase domain region) and FLT-1 (FMS-liketyrosine kinase) receptors. These receptors exist only on endothelial(vascular) cells. As cells become depleted in oxygen, because of traumaand the like, VEGF production increases in such cells which then bind tothe respective receptors in order to signal ultimate biological effect.The signal then increases vascular permeability and the cells divide andexpand to form new vascular pathways-vasculogenesis and angiogenesis.Thus, VEGF and derivatives thereof, as described in the patentapplications referred to supra, would find use in the restoration ofvasculature after a myocardial infarct, as well as other uses that canbe deduced.

The present invention is predicated upon research intended to identifythe regions or domains that are responsible for binding to the KDR andFLT receptors. After identification, it was a goal to mutagenize such adomain in order to produce variants that have either increased ordecreased binding capability with respect to those respective KDR andFLT binding domains.

It was a further object of this research to produce VEGF variants thatwould have selective activity with respect to the binding KDR and FLTdomains. It was postulated that if one could increase the bindingcapability of the domain responsible for vasculogenesis andangiogenesis, one could produce a more potent material for intendedtherapeutic use. Conversely, if one could by induced mutagenesis produceVEGF variants that had reduced activity, and consequently,anti-vasculogenesis and anti-angiogenesis, one could use such variantsin instances of tumor treatment in order to starve the tumors forintended regression.

As further objects, such variants could then be employed in assaysystems to discover small molecule agonists and antagonists for intendedtherapeutic use in such indications.

The results of such research is the subject of the present invention.The dominant domains of VEGF for receptor binding were found to beproximately located, but at distinct sites, allowing the development ofvariants that proved to be receptor-selective. The KDR receptor wasfound to bind VEGF predominantly through the sites on a punitive loopwhich contains Arginine (Arg or R) at position 82 of VEGF, Lysine (Lysor K) at position 84 and Histidine (His or H) at position 86. The FLT-1receptor was found to bind VEGF predominantly through the sites on aputative loop which contains Aspartic acid (Asp or D) at position 63,Glutamic acid (Glu or E) at position 64 and Glutamic acid (Glu or E) atposition 67. Mutagenesis experiments followed with respect generally tothese domains resulting in the variants of the present invention. Suchmutagenesis employed both specific and random strategies, in accordancewith procedures generally well known to the art-skilled.

SUMMARY OF THE INVENTION

The objects of this invention, as defined generally supra, are achievedby the provision of a vascular endothelial cell growth factor (VEGF)variant having mutations in the Kinase domain region (KDR) and/or theFMS-like Tyrosine-Kinase region (FLT-1), said variants exhibitingmodified binding characteristics at said regions compared with nativeVEGF.

In a preferred embodiment, such mutagenesis is effected within theregion bounded by amino acids within the approximate positions 78 to 95of VEGF.

In another embodiment, such mutagenesis is effected within the regionbounded by amino acids within the approximate positions 60 to 70 ofVEGF.

In another embodiment such mutagenesis is effected at both said regions.

In a particularly preferred embodiment, mutagenesis is effected at leastat positions 82, 84 and 86 of VEGF and/or positions 63, 64 and 67 ofVEGF.

In still another particularly preferred embodiment, VEGF variants areproduced in which mutagenesis is created at positions 82, 84 and 86 asfollows: R82A, K84A and H86A and/or D63A, E64A and E67A. These symbolssignify the change made at the respective positions, for example, theArginine (R) codon at position 82 was mutated to produce an Alanine (A)at that position, etc.

In other embodiments, the present invention relates to DNA sequencesencoding the various variants described supra, replicable expressionvectors capable of expressing said DNA sequences via transforming DNA ina transformant host cell, and microorganisms and cell cultures which aretransformed with such vectors.

In yet further embodiments, the present invention is directed tocompositions useful for treating indications where vasculogenesis orangiogenesis is desired for treatment of the underlying disease statecomprising a therapeutically effective amount of a VEGF variant hereofin admixture with a pharmaceutically acceptable carrier.

In still another embodiment, the present invention is directed to acomposition for treating indications where antivascular-genesis orantiangio-genesis is desired, such as in arresting tumors, comprising atherapeutically effective amount of a variant hereof in admixture with apharmaceutically acceptable carrier.

In particular, mutations in accordance with the present invention thathave been introduced generally at positions spanning the region of aminoacids 78 to 95, and more particularly 82 to 86, create variants thatbind normally to the FLT receptor but have significantly reduced bindingproperties with respect to the KDR receptor. Mutations in accordancewith the present invention that have been introduced generally atpositions spanning the region of amino acids 60 to 70, and moreparticularly 63 to 67, create variants that bind essentially normally tothe KDR receptor but have significantly reduced binding with respect tothe FLT receptor.

Expanding on the basic premise hereof of the discovery and mutagenesisof the KDR and/or FLT binding domains of VEGF, the present invention isdirected to all associated embodiments deriving therefrom, includingrecombinant DNA materials and processes for preparing such variants,materials and information for compounding such variants intopharmaceutically finished form and assays using such variants to screenfor candidates that have agonistic or antagonistic properties withrespect to the KDR and/or FLT receptors.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts both the amino acid and DNA sequence for VEGF having 165amino acids. Predicted amino acids of the protein are shown below theDNA sequence and are numbered from the first residue of the N-terminusof the protein sequence. Negative amino acid numbers refer to thepresumed leader signal sequence or pre-protein, while positive numbersrefer to the putative mature protein.

FIG. 2 depicts the various domains of VEGF₁₆₅ and shows the plasmincleavage site. The receptor binding domains are located within theregion spanning amino acids 1 to 110.

FIG. 3 displays the separate and distinct receptor binding sites for theKDR and FLT receptors. These sites are located respectively in theregion spanning generally amino acids 78 to 90 (depicted as “A” in FIG.3) and 60 to 70 (depicted as “B”).

FIG. 4 shows the KDR receptor binding being mediated by the 1-110 dimerof VEGF.

FIG. 5 shows the charged-to-Alanine scan mutations hereof in VEGF.

FIG. 6 shows that KDR-binding is primarily mediated by R82, K84, H86.IC50 refers to the 50 % inhibitory concentration which is related to thedisassociation constant.

FIG. 7 shows that FLT-binding is primarily mediated by D63, E64, E67.

FIG. 8 shows that extra glycosylation at position 82 blocks KDR-binding.

FIG. 9 shows that mutations in the 82-86 site block KDR-binding (A) andthat mutations in the 63-67 site block FLT-binding (B).

FIG. 10 shows that multiple mutations have a synergistic effect withKDR: K84A is a potent single Alanine substitution.

FIG. 11 shows that VEGF mutants with decreased KDR receptor binding areweak endothelial cell mitogens.

FIG. 12 is a color photograph of a molecular model of VEGF showing thelocations of the KDR-(blue) and FLT-(red)binding sites.

FIG. 13 depicts the construction with its various elements of theplasmid pSDVF₁₆₅.

FIG. 14 depicts the construction with its various elements of theplasmid pRK5.

FIG. 15 depicts the construction schematic followed to prepare the finalexpression vectors harboring DNA that contains mutations in accordancewith preparing the various products of the present invention.

FIG. 16 depicts the KDR-IgG binding levels of various VEGF variants.

FIG. 17 depicts the FLT-1-IgG binding levels of various VEGF variants.

FIG. 18 depicts the A461-IgG binding levels of various VEGF variants.

FIG. 19 shows the quantitation of VEGF mutants by monoclonal- andpolyclonal-based ELISA. Aliquots of conditioned cell media with VEGF orVEGF mutants were analyzed by immunoassay using two types of ELISA. Apolyclonal anti-VEGF antibody combined with a monoclonal antibody (Mab5F8, specific to the carboxy-terminal domain of VEGF) yielded asandwich-type immunoassay that was unaffected by mutations in thereceptor-binding domain of VEGF (1-110 region). Alternatively, a dualmonoclonal based ELISA with Mabs 5F8 and A4.6.1 was used to quantify theVEGF mutants. The immunoassay results of multiple transfections (2 to 10replicates) were averaged for each mutant and compared in FIG. 19.

FIG. 20 shows the SDS-PAGE Immunoblot of VEGF mutants. Transienttransfection supernatants (from 293 cells) containing approximately 10to 20 ng of VEGF or VEGF mutant were analyzed by non-reduced SDS-PAGE.The gels were transferred and blotted as described in the ExperimentalProcedures, using a panel of 5 murine monoclonal antihuman VEGF₁₆₅antibodies identified as the following: 2E3, 4D7, A4.6.1, 5C3, and 5F8.The immunoblots were exposed for 5 days.

FIG. 21 shows activity of VEGF mutants in endothelial cell growth assay.The VEGF mutants were expressed in 293 cell culture, the conditionedcell media was used to stimulate mitogenesis of bovine adrenal corticalcapillary endothelial cells. The mean residue number indicates thelocation of the mutations. The values are expressed as the concentrationrequired to half-maximally stimulate endothelial cell proliferation(EC₅₀). Alanine mutants of VEGF are indicated as filled circles andpotential extra-glycosylated VEGF mutants are filled boxes. Theseexperiments were done in triplicate.

DETAILED DESCRIPTION OF THE INVENTION

A. Definitions

As used herein, “vascular endothelial cell growth factor,” or “VEGF,”refers to a mammalian growth factor as defined in U.S. Pat. No.5,332,671, including the human amino acid sequence of FIG. 1. Thebiological activity of native VEGF is shared by any analogue or variantthereof that is capable of promoting selective growth of vascularendothelial cells but not of bovine corneal endothelial cells, lensepithelial cells, adrenal cortex cells, BHK-21 fibroblasts, orkeratinocytes, or that possesses an immune epitope that isimmunologically cross-reactive with an antibody raised against at leastone epitope of the corresponding native VEGF.

“Transfection” refers to the taking up of an expression vector by a hostcell whether or not any coding sequences are in fact expressed. Numerousmethods of transfection are known to the ordinarily skilled artisan, forexample, CaPO₄ and electroporation. Successful transfection is generallyrecognized when any indication of the operation of this vector occurswithin the host cell.

“Transformation” means introducing DNA into an organism so that the DNAis replicable, either as an extrachromosomal element or by chromosomalintegrant. Depending on the host cell used, transformation is done usingstandard techniques appropriate to such cells. The calcium treatmentemploying calcium chloride, as described by Cohen, S. N. Proc. Natl.Acad. Sci. (USA), 69, 2110 (1972) and Mandel et al. J. Mol. Biol. 53,154 (1970), is generally used for prokaryotes or other cells thatcontain substantial cell-wall barriers. For mammalian cells without suchcell walls, the calcium phosphate precipitation method of Graham, F. andvan der Eb, A., Virology, 52, 456-457 (1978) is preferred. Generalaspects of mammalian cell host system transformations have beendescribed by Axel in U.S. Pat. No. 4,399,216 issued Aug. 16, 1983.Transformations into yeast are typically carried out according to themethod of Van Solingen, P., et al. J. Bact., 130, 946 (1977) and Hsiao,C. L., et al. Proc. Natl. Acad. Sci. (USA) 76, 3829 (1979). However,other methods for introducing DNA into cells such as by nuclearinjection or by protoplast fusion may also be used.

“Site-directed mutagenesis” is a technique standard in the art, and isconducted using a synthetic oligonucleotide primer complementary to asingle-stranded phage DNA to be mutagenized except for limitedmismatching, representing the desired mutation. Briefly, the syntheticoligonucleotide is used as a primer to direct synthesis of a strandcomplementary to the phage, and the resulting double-stranded DNA istransformed into a phage-supporting host bacterium. Cultures of thetransformed bacteria are plated in top agar, permitting plaque formationfrom single cells that harbor the phage. Theoretically, 50% of the newplaques will contain the phage having, as a single strand, the mutatedform; 50% will have the original sequence. The plaques are hybridizedwith kinased synthetic primer at a temperature that permitshybridization of an exact match, but at which the mismatches with theoriginal strand are sufficient to prevent hybridization. Plaques thathybridize with the probe are then selected and cultured, and the DNA isrecovered.

“Operably linked” refers to juxtaposition such that the normal functionof the components can be performed. Thus, a coding sequence “operablylinked” to control sequences refers to a configuration wherein thecoding sequence can be expressed under the control of these sequencesand wherein the DNA sequences being linked are contiguous and, in thecase of a secretory leader, contiguous and in reading phase. Forexample, DNA for a presequence or secretory leader is operably linked toDNA for a polypeptide if it is expressed as a preprotein thatparticipates in the secretion of the polypeptide; a promoter or enhanceris operably linked to a coding sequence if it affects the transcriptionof the sequence; or a ribosome binding site is operably linked to acoding sequence if it is positioned so as to facilitate translation.Linking is accomplished by ligation at convenient restriction sites. Ifsuch sites do not exist, then synthetic oligonucleotide adaptors orlinkers are used in accord with conventional practice.

“Control sequences” refers to DNA sequences necessary for the expressionof an operably linked coding sequence in a particular host organism. Thecontrol sequences that are suitable for prokaryotes, for example,include a promoter, optionally an operator sequence, a ribosome bindingsite, and possibly, other as yet poorly understood sequences. Eukaryoticcells are known to utilize promoters, polyadenylation signals, andenhancers.

“Expression system” refers to DNA sequences containing a desired codingsequence and control sequences in operable linkage, so that hoststransformed with these sequences are capable of producing the encodedproteins. To effect transformation, the expression system may beincluded on a vector; however, the relevant DNA may then also beintegrated into the host chromosome.

As used herein, “cell,” “cell line,” and “cell culture” are usedinterchangeably and all such designations include progeny. Thus,“transformants” or “transformed cells” includes the primary subject celland cultures derived therefrom without regard for the number oftransfers. It is also understood that all progeny may not be preciselyidentical in DNA content, due to deliberate or inadvertent mutations.Mutant progeny that have the same functionality as screened for in theoriginally transformed cell are included. Where distinct designationsare intended, it will be clear from the context.

“Plasmids” are designated by a lower case p preceded and/or followed bycapital letters and/or numbers. The starting plasmids herein arecommercially available, are publicly available on an unrestricted basis,or can be constructed from such available plasmids in accord withpublished procedures. In addition, other equivalent plasmids are knownin the art and will be apparent to the ordinary artisan.

“Digestion” of DNA refers to catalytic cleavage of the DNA with anenzyme that acts only at certain locations in the DNA. Such enzymes arecalled restriction enzymes, and the sites for which each is specific iscalled a restriction site. The various restriction enzymes used hereinare commercially available and their reaction conditions, cofactors, andother requirements as established by the enzyme suppliers are used.Restriction enzymes commonly are designated by abbreviations composed ofa capital letter followed by other letters representing themicroorganism from which each restriction enzyme originally was obtainedand then a number designating the particular enzyme. In general, about 1mg of plasmid or DNA fragment is used with about 1-2 units of enzyme inabout 20 ml of buffer solution. Appropriate buffers and substrateamounts for particular restriction enzymes are specified by themanufacturer. Incubation of about 1 hour at 37° C. is ordinarily used,but may vary in accordance with the supplier's instructions. Afterincubation, protein is removed by extraction with phenol and chloroform,and the digested nucleic acid is recovered from the aqueous fraction byprecipitation with ethanol. Digestion with a restriction enzymeinfrequently is followed with bacterial alkaline phosphatase hydrolysisof the terminal 5′ phosphates to prevent the two restriction cleavedends of a DNA fragment from “circularizing” or forming a closed loopthat would impede insertion of another DNA fragment at the restrictionsite. Unless otherwise stated, digestion of plasmids is not followed by5′ terminal dephosphorylation. Procedures and reagents fordephosphorylation are conventional (T. Maniatis et al. 1982, MolecularCloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory,1982) pp. 133-134).

“Recovery” or “isolation” of a given fragment of DNA from a restrictiondigest means separation of the digest on polyacrylamide or agarose gelby electrophoresis, identification of the fragment of interest bycomparison of its mobility versus that of marker DNA fragments of knownmolecular weight, removal of the gel section containing the desiredfragment, and separation of the gel from DNA. This procedure is knowngenerally. For example, see R. Lawn et al., Nucleic Acids Res. 9,6103-6114 (1981), and D. Goeddel et al., Nucleic Acids Res. 8, 4057(1980).

“Southern Analysis” is a method by which the presence of DNA sequencesin a digest or DNA-containing composition is confirmed by hybridizationto a known, labelled oligonucleotide or DNA fragment. For the purposesherein, unless otherwise provided, Southern analysis shall meanseparation of digests on 1 percent agarose, denaturation, and transferto nitrocellulose by the method of E. Southern, J. Mol. Biol. 98,503-517 (1975), and hybridization as described by T. Maniatis et al.,Cell 15, 687-701 (1978).

“Ligation” refers to the process of forming phosphodiester bonds betweentwo double stranded nucleic acid fragments (T. Maniatis et al. 1982,supra, p. 146). Unless otherwise provided, ligation may be accomplishedusing known buffers and conditions with 10 units of T4 DNA ligase(“ligase”) per 0.5 mg of approximately equimolar amounts of the DNAfragments to be ligated.

“Preparation” of DNA from transformants means isolating plasmid DNA frommicrobial culture. Unless otherwise provided, the alkaline/SDS method ofManiatis et al. 1982, supra, p. 90, may be used.

“Oligonucleotides” are short-length, single- or double-strandedpolydeoxynucleotides that are chemically synthesized by known methods(such as phosphotriester, phosphite, or phosphoramidite chemistry, usingsolid phase techniques such as described in EP Pat. Pub. No. 266,032published May 4, 1988, or via deoxynucleoside H-phosphonateintermediates as described by Froehler et al., Nucl. Acids Res. 14,5399-5407 [1986]). They are then purified on polyacrylamide gels.

The abbreviation “KDR” refers to the kinase domain region of the VEGFmolecule. It is this region which is known to bind to the kinase domainregion receptor.

The abbreviation “FLT-1” refers to the FMS-like tyrosine kinase bindingdomain which is known to bind to the corresponding FLT-1 receptor. Thesereceptors exist on the surfaces of endothelial cells.

B. General Methodology

1. Glycosylation

The VEGF amino acid sequence variant may contain at least one amino acidsequence that has the potential to be glycosylated through an N-linkageand that is not normally glycosylated in the native molecule.

Introduction of an N-linked glycosylation site in the variant requires atripeptidyl sequence of the formula: asparagine-X-serine orasparagine-X-threonine, wherein asparagine is the acceptor and X is anyof the twenty genetically encoded amino acids except proline, whichprevents glycosylation. See D. K. Struck and W. J. Lennarz, in TheBiochemistry of Glycoproteins and Proteoglycans, ed. W. J. Lennarz,Plenum Press, 1980, p. 35; R. D. Marshall, Biochem. Soc. Symp., 40, 17(1974), and Winzler, R. J., in Hormonal Proteins and Peptides (ed. Li,C. I.) p. 1-15 (Academic Press, New York, 1973). The amino acid sequencevariant herein is modified by substituting for the amino acid(s) at theappropriate site(s) the appropriate amino acids to effect glycosylation.

If O-linked glycosylation is to be employed, O-glycosidic linkage occursin animal cells between N-acetylgalactosamine, galactose, or xylose andone of several hydroxyamino acids, most commonly serine or threonine,but also in some cases a 5-hydroxyproline or 5-hydroxylysine residueplaced in the appropriate region of the molecule.

Glycosylation patterns for proteins produced by mammals are described indetail in The Plasma Proteins: Structure, Function and Genetic Control,F. W. Putnam, ed., 2nd edition, volume 4 (Academic Press, New York,1984), p. 271-315, the entire disclosure of which is incorporated hereinby reference. In this chapter, asparagine-linked oligosaccharides arediscussed, including their subdivision into at least three groupsreferred to as complex, high mannose, and hybrid structures, as well asO-glucosidically linked oligosaccharides.

Chemical and/or enzymatic coupling of glycosides to proteins can beaccomplished using a variety of activated groups, for example, asdescribed by Aplin and Wriston in CRC Crit. Rev. Biochem., pp. 259-306(1981), the disclosure of which is incorporated herein by reference. Theadvantages of the chemical coupling techniques are that they arerelatively simple and do not need the complicated enzymatic machineryrequired for natural O- and N-linked glycosylation. Depending on thecoupling mode used, the sugar(s) may be attached to (a) arginine orhistidine, (b) free carboxyl groups such as those of glutamic acid oraspartic acid, (c) free sulfhydryl groups such as those of cysteine, (d)free hydroxyl groups such as those of serine, threonine, orhydroxyproline, (e) aromatic residues such as those of phenylalanine,tyrosine, or tryptophan, or (f) the amide group of glutamine. Thesemethods are described more fully in PCT WO 87/05330 published Sep. 11,1987, the disclosure of which is incorporated herein by reference.

Glycosylation patterns for proteins produced by yeast are described indetail by Tanner and Lehle, Biochim. Biophys. Acta, 906(1), 81-99 (1987)and by Kukuruzinska et al., Annu. Rev. Biochem., 56, 915-944(1987), thedisclosures of which are incorporated herein by reference.

2. Amino Acid Sequence Variants

a. Additional Mutations

For purposes of shorthand designation of VEGF variants described herein,it is noted that numbers refer to the amino acid residue/position alongthe amino acid sequences of putative mature VEGF. Amino acididentification uses the single-letter alphabet of amino acids, i.e., AspD Aspartic acid Ile I Isoleucine Thr T Threonine Leu L Leucine Ser SSerine Tyr Y Tyrosine Glu E Glutamic acid Phe F Phenylalanine Pro PProline His H Histidine Gly G Glycine Lys K Lysine Ala A Alanine Arg RArginine Cys C Cysteine Trp W Tryptophan Val V Valine Gln Q GlutamineMet M Methionine Asn N Asparagine

The present invention is directed to variants of VEGF where suchvariants have modifications in the amino acid sequence in two of thereceptor binding domains: 1) from within the range of amino acid ofabout 78 to 95 and 2) in the range of amino acid at position about 60 to70. These variants have selective activity with respect to therespective binding sites of the corresponding receptors.

It will be appreciated that certain other variants at other positions inthe VEGF molecule can be made without departing from the spirit of thepresent invention with respect to the two receptor binding sitevariations. Thus point mutational or other broader variations may bemade in all other parts of the molecule so as to impart interestingproperties that do not effect the overall properties of the variantswith respect to the domains from 78 to 95 and 60 to 70.

These latter, additional variants may be made by means generally knownwell in the art.

For example covalent modifications may be made to various of the aminoacid residues.

Cysteinyl residues most commonly are reacted with a-haloacetates (andcorresponding amines), such as chloroacetic acid or chloroacetamide, togive carboxymethyl or carboxyamidomethyl derivatives. Cysteinyl residuesalso are derivatized by reaction with bromotrifluoroacetone,a-bromo-b-(5-imidozoyl)propionic acid, chloroacetyl phosphate,N-alkylmaleimides, 3-nitro-2-pyridyl disulfide, methyl 2-pyridyldisulfide, p-chloromercuribenzoate, 2-chloromercuri-4-nitrophenol, orchloro-7-nitrobenzo-2-oxa-1,3-diazole.

Histidyl residues are derivatized by reaction with diethylpyrocarbonateat pH 5.5-7.0 because this agent is relatively specific for the histidylside chain. Para-bromophenacyl bromide also is useful; the reaction ispreferably performed in 0.1M sodium cacodylate at pH 6.0.

Lysinyl and amino terminal residues are reacted with succinic or othercarboxylic acid anhydrides. Derivatization with these agents has theeffect of reversing the charge of the lysinyl residues. Other suitablereagents for derivatizing a-amino-containing residues includeimidoesters such as methyl picolinimidate; pyridoxal phosphate;pyridoxal; chloroborohydride; trinitrobenzenesulfonic acid;O-methylisourea; 2,4-pentanedione; and transaminase-catalyzed reactionwith glyoxylate.

Arginyl residues are modified by reaction with one or severalconventional reagents, among them phenylglyoxal, 2,3-butanedione,1,2-cyclohexanedione, and ninhydrin. Derivatization of arginine residuesrequires that the reaction be performed in alkaline conditions becauseof the high pK_(a) of the guanidine functional group. Furthermore, thesereagents may react with the groups of lysine as well as the arginineepsilon-amino group.

The specific modification of tyrosyl residues per se has been studiedextensively, with particular interest in introducing spectral labelsinto tyrosyl residues by reaction with aromatic diazonium compounds ortetranitromethane. Most commonly, N-acetylimidizol and tetranitromethaneare used to form O-acetyl tyrosyl species and 3-nitro derivatives,respectively. Tyrosyl residues are iodinated using ¹²⁵I or ¹³¹I toprepare labeled proteins for use in radioimmunoassay, the chloramine Tmethod described above being suitable.

Carboxyl side groups (aspartyl or glutamyl) are selectively modified byreaction with carbodiimides (R′-N-C-N-R′) such as1-cyclohexyl-3-(2-morpholinyl-(4-ethyl) carbodiimide or1-ethyl-3-(4-azonia-4,4-dimethylpentyl) carbodiimide. Furthermore,aspartyl and glutamyl residues are converted to asparaginyl andglutaminyl residues by reaction with ammonium ions.

Derivatization with bifunctional agents is useful for crosslinking theVEGF to a water-insoluble support matrix or surface for use in themethod for purifying anti-VEGF antibodies. Commonly used crosslinkingagents include, e.g., 1,1-bis(diazoacetyl)-2-phenylethane,glutaraldehyde, N-hydroxysuccinimide esters, for example, esters with4-azidosalicylic acid, homobifunctional imidoesters, includingdisuccinimidyl esters such as 3,3′-dithiobis(succinimidylpropionate),and bifunctional maleimides such as bis-N-maleimido-1,8-octane.Derivatizing agents such asmethyl-3-[(p-azidophenyl)dithio]propioimidate yield photoactivatableintermediates that are capable of forming crosslinks in the presence oflight. Alternatively, reactive water-insoluble matrices such as cyanogenbromide-activated carbohydrates and the reactive substrates described inU.S. Pat. Nos. 3,969,287; 3,691,016; 4,195,128; 4,247,642; 4,229,537;and 4,330,440 are employed for protein immobilization.

Glutaminyl and asparaginyl residues are frequently deamidated to thecorresponding glutamyl and aspartyl residues. Alternatively, theseresidues are deamidated under mildly acidic conditions. Either form ofthese residues falls within the scope of this invention.

Other modifications include hydroxylation of proline and lysine,phosphorylation of hydroxyl groups of seryl or threonyl residues,methylation of the a-amino groups of lysine, arginine, and histidineside chains (T. E. Creighton, Proteins: Structure and MolecularProperties, W.H. Freeman & Co., San Francisco, pp. 79-86 [1983]),acetylation of the N-terminal amine, and, in some instances, amidationof the C-terminal carboxyl group.

b. DNA Mutations

Amino acid sequence variants of VEGF can also be prepared by mutationsin the DNA. Such variants include, for example, deletions from, orinsertions or substitutions of, residues within the amino acid sequenceshown in FIG. 1. Any combination of deletion, insertion, andsubstitution may also be made to arrive at the final construct, providedthat the final construct possesses the desired activity. Obviously, themutations that will be made in the DNA encoding the variant must notplace the sequence out of reading frame and preferably will not createcomplementary regions that could produce secondary mRNA structure (seeEP 75,444A).

At the genetic level, these variants ordinarily are prepared bysite-directed mutagenesis of nucleotides in the DNA encoding the VEGF,thereby producing DNA encoding the variant, and thereafter expressingthe DNA in recombinant cell culture. The variants typically exhibit thesame qualitative biological activity as the naturally occurring analog.

While the site for introducing an amino acid sequence variation ispredetermined, the mutation per se need not be predetermined. Forexample, to optimize the performance of a mutation at a given site,random mutagenesis may be conducted at the target codon or region andthe expressed VEGF variants screened for the optimal combination ofdesired activity. Techniques for making substitution mutations atpredetermined sites in DNA having a known sequence are well known, forexample, site-specific mutagenesis.

Preparation of VEGF variants in accordance herewith is preferablyachieved by site-specific mutagenesis of DNA that encodes an earlierprepared variant or a nonvariant version of the protein. Site-specificmutagenesis allows the production of VEGF variants through the use ofspecific oligonucleotide sequences that encode the DNA sequence of thedesired mutation, as well as a sufficient number of adjacentnucleotides, to provide a primer sequence of sufficient size andsequence complexity to form a stable duplex on both sides of thedeletion junction being traversed. Typically, a primer of about 20 to 25nucleotides in length is preferred, with about 5 to 10 residues on bothsides of the junction of the sequence being altered. In general, thetechnique of site-specific mutagenesis is well known in the art, asexemplified by publications such as Adelman et al., DNA 2, 183 (1983),the disclosure of which is incorporated herein by reference.

As will be appreciated, the site-specific mutagenesis techniquetypically employs a phage vector that exists in both a single-strandedand double-stranded form. Typical vectors useful in site-directedmutagenesis include vectors such as the M13 phage, for example, asdisclosed by Messing et al., Third Cleveland Symposium on Macromoleculesand Recombinant DNA, Editor A. Walton, Elsevier, Amsterdam (1981), thedisclosure of which is incorporated herein by reference. These phage arereadily commercially available and their use is generally well known tothose skilled in the art. Alternatively, plasmid vectors that contain asingle-stranded phage origin of replication (Veira et al., Meth.Enzymol, 153, 3 [1987]) may be employed to obtain single-stranded DNA.

In general, site-directed mutagenesis in accordance herewith isperformed by first obtaining a single-stranded vector that includeswithin its sequence a DNA sequence that encodes the relevant protein. Anoligonucleotide primer bearing the desired mutated sequence is prepared,generally synthetically, for example, by the method of Crea et al.,Proc. Natl. Acad. Sci. (USA), 75, 5765 (1978). This primer is thenannealed with the single-stranded protein-sequence-containing vector,and subjected to DNA-polymerizing enzymes such as E. coli polymerase IKlenow fragment, to complete the synthesis of the mutation-bearingstrand. Thus, a heteroduplex is formed wherein one strand encodes theoriginal non-mutated sequence and the second strand bears the desiredmutation. This heteroduplex vector is then used to transform appropriatecells such as JM101 cells and clones are selected that includerecombinant vectors bearing the mutated sequence arrangement.

After such a clone is selected, the mutated protein region may beremoved and placed in an appropriate vector for protein production,generally an expression vector of the type that may be employed fortransformation of an appropriate host.

c. Types of Mutations

Amino acid sequence deletions generally range from about 1 to 30residues, more preferably 1 to 10 residues, and typically arecontiguous.

Amino acid sequence insertions include amino- and/or carboxyl-terminalfusions of from one residue to polypeptides of essentially unrestrictedlength, as well as intrasequence insertions of single or multiple aminoacid residues. Intrasequence insertions (i.e., insertions within themature VEGF sequence) may range generally from about 1 to 10 residues,more preferably 1 to 5. An example of a terminal insertion includes afusion of a signal sequence, whether heterologous or homologous to thehost cell, to the N-terminus of the VEGF molecule to facilitate thesecretion of mature VEGF from recombinant hosts.

The third group of variants are those in which at least one amino acidresidue in the VEGF molecule, and preferably only one, has been removedand a different residue inserted in its place. Such substitutionspreferably are made in accordance with the following Table 1 when it isdesired to modulate finely the characteristics of a VEGF molecule. TABLE1 Original Exemplary Residue Substitutions Ala (A) gly; ser Arg (R) lysAsn (N) gln; his Asp (D) glu Cys (C) ser Gln (Q) asn Glu (E) asp Gly (G)ala; pro His (H) asn; gln Ile (I) leu; val Leu (L) ile; val Lys (K) arg;gln; glu Met (M) leu; tyr; ile Phe (F) met; leu; tyr Ser (S) thr Thr (T)ser Trp (W) tyr Tyr (Y) trp; phe Val (V) ile; leu

Substantial changes in function or immunological identity are made byselecting substitutions that are less conservative than those in TableI, i.e., selecting residues that differ more significantly in theireffect on maintaining (a) the structure of the polypeptide backbone inthe area of the substitution, for example, as a sheet or helicalconformation, (b) the charge or hydrophobicity of the molecule at thetarget site, or (c) the bulk of the side chain. The substitutions thatin general are expected to produce the greatest changes in VEGFproperties will be those in which (a) glycine and/or proline (P) issubstituted by another amino acid or is deleted or inserted; (b) ahydrophilic residue, e.g., seryl or threonyl, is substituted for (or by)a hydrophobic residue, e.g., leucyl, isoleucyl, phenylalanyl, valyl, oralanyl; (c) a cysteine residue is substituted for (or by) any otherresidue; (d) a residue having an electropositive side chain, e.g.,lysyl, arginyl, or histidyl, is substituted for (or by) a residue havingan electronegative charge, e.g., glutamyl or aspartyl; (e) a residuehaving an electronegative side chain is substituted for (or by) aresidue having an electropositive charge; or (f) a residue having abulky side chain, e.g., phenylaianine, is substituted for (or by) onenot having such a side chain, e.g., glycine.

Most deletions and insertions, and substitutions in particular, are notexpected to produce radical changes in the characteristics of the VEGFmolecule. However, when it is difficult to predict the exact effect ofthe substitution, deletion, or insertion in advance of doing so, oneskilled in the art will appreciate that the effect will be evaluated byroutine screening assays. For example, a variant typically is made bysite-specific mutagenesis of the native VEGF-encoding nucleic acid,expression of the variant nucleic acid in recombinant cell culture, and,optionally, purification from the cell culture, for example, byimmunoaffinity adsorption on a rabbit polyclonal anti-VEGF column (toabsorb the variant by binding it to at least one remaining immuneepitope).

Since VEGF tends to aggregate into dimers, it is within the scope hereofto provide hetero- and homodimers, wherein one or both subunits arevariants. Where both subunits are variants, the changes in amino acidsequence can be the same or different for each subunit chain.Heterodimers are readily produced by cotransforming host cells with DNAencoding both subunits and, if necessary, purifying the desiredheterodimer, or by separately synthesizing the subunits, dissociatingthe subunits (e.g., by treatment with a chaotropic agent such as urea,guanidine hydrochloride, or the like), mixing the dissociated subunits,and then reassociating the subunits by dialyzing away the chaotropicagent.

Also included within the scope of mutants herein are so-calledglyco-scan mutants. This embodiment takes advantage of the knowledge ofso-called glycosylation sites which are identified by thesequence-NXS_(T)

wherein N represents the amino acid asparagine, X represents any aminoacid except proline and probably glysine and the third position can beoccupied by either amino acid serine or threonine. Thus, whereappropriate such a glycosylation site can be introduced so as to producea species containing glycosylation moieties at that position. Similarly,an existing glycosylation site can be removed by mutation so as toproduce a species that is devoid of glycosylation at that site. It willbe understood, again, as with the other mutations contemplated by thepresent invention, that they are introduced within the so-called KDRand/or FLT-1 domains in accord with the basic premise of the presentinvention, and they can be introduced at other locations outside ofthese domains within the overall molecule so long as the final productdoes not differ in overall kind from the properties of the mutationintroduced in one or both of said two binding domains.

The activity of the cell lysate or purified VEGF variant is thenscreened in a suitable screening assay for the desired characteristic.For example, a change in the immunological character of the VEGFmolecule, such as affinity for a given antibody, is measured by acompetitive-type immunoassay. Changes in the enhancement or suppressionof vascular endothelium growth by the candidate mutants are measured bythe appropriate assay. Modifications of such protein properties as redoxor thermal stability, hydrophobicity, susceptibility to proteolyticdegradation, or the tendency to aggregate with carriers or intomultimers are assayed by methods well known to the ordinarily skilledartisan.

3. Recombinant Expression

The VEGF molecule desired may be prepared by any technique, includingrecombinant methods. Likewise, an isolated DNA is understood herein tomean chemically synthesized DNA, cDNA, chromosomal, or extrachromosomalDNA with or without the 3′- and/or 5′-flanking regions. Preferably, thedesired VEGF herein is made by synthesis in recombinant cell culture.

For such synthesis, it is first necessary to secure nucleic acid thatencodes a VEGF. DNA encoding a VEGF molecule may be obtained from bovinepituitary follicular cells by (a) preparing a cDNA library from thesecells, (b) conducting hybridization analysis with labeled DNA encodingthe VEGF or fragments thereof (up to or more than 100 base pairs inlength) to detect clones in the library containing homologous sequences,and (c) analyzing the clones by restriction enzyme analysis and nucleicacid sequencing to identify full-length clones. DNA that is capable ofhybridizing to a VEGF-encoding DNA under low stringency conditions isuseful for identifying DNA encoding VEGF. Both high and low stringencyconditions are defined further below. If full-length clones are notpresent in a cDNA library, then appropriate fragments may be recoveredfrom the various clones using the nucleic acid sequence informationdisclosed herein for the first time and ligated at restriction sitescommon to the clones to assemble a full-length clone encoding the VEGF.Alternatively, genomic libraries will provide the desired DNA. Thesequence of the DNA encoding bovine VEGF that was ultimately determinedis shown in FIG. 2. The sequence of the DNA encoding human VEGF that wasultimately determined by probing a human leukemia cell line is shown inFIG. 10.

Once this DNA has been identified and isolated from the library it isligated into a replicable vector for further cloning or for expression.

In one example of a recombinant expression system a VEGF-encoding geneis expressed in mammalian cells by transformation with an expressionvector comprising DNA encoding the VEGF. It is preferable to transformhost cells capable of accomplishing such processing so as to obtain theVEGF in the culture medium or periplasm of the host cell, i.e., obtain asecreted molecule.

a. Useful Host Cells and Vectors

The vectors and methods disclosed herein are suitable for use in hostcells over a wide range of prokaryotic and eukaryotic organisms.

In general, of course, prokaryotes are preferred for the initial cloningof DNA sequences and construction of the vectors useful in theinvention. For example, E. coli K12 strain MM 294 (ATCC No. 31,446) isparticularly useful. Other microbial strains that may be used include E.coli strains such as E. coli B and E. coli X1776 (ATCC No. 31,537).These examples are, of course, intended to be illustrative rather thanlimiting.

Prokaryotes may also be used for expression. The aforementioned strains,as well as E. coli strains W3110 (F-, lambda-, prototrophic, ATCC No.27,325), K5772 (ATCC No. 53,635), and SR101, bacilli such as Bacillussubtilis, and other enterobacteriaceae such as Salmonella typhimurium orSerratia marcesans, and various pseudomonas species, may be used.

In general, plasmid vectors containing replicon and control sequencesthat are derived from species compatible with the host cell are used inconnection with these hosts. The vector ordinarily carries a replicationsite, as well as marking sequences that are capable of providingphenotypic selection in transformed cells. For example, E. coli istypically transformed using pBR322, a plasmid derived from an E. colispecies (see, e.g., Bolivar et al., Gene 2, 95 [1977]). pBR322 containsgenes for ampicillin and tetracycline resistance and thus provides easymeans for identifying transformed cells. The pBR322 plasmid, or othermicrobial plasmid or phage, must also contain, or be modified tocontain, promoters that can be used by the microbial organism forexpression of its own proteins.

Those promoters most commonly used in recombinant DNA constructioninclude the b-lactamase (penicillinase) and lactose promoter systems(Chang et al., Nature, 375, 615 [1978]; Itakura et al., Science, 198,1056 [1977]; Goeddel et al., Nature, 281, 544 [1979]) and a tryptophan(trp) promoter system (Goeddel et al., Nucleic Acids Res., 8, 4057[1980]; EPO Appl. Publ. No. 0036,776). While these are the most commonlyused, other microbial promoters have been discovered and utilized, anddetails concerning their nucleotide sequences have been published,enabling a skilled worker to ligate them functionally with plasmidvectors (see, e.g., Siebenlist et al., Cell, 20, 269 [1980]).

In addition to prokaryotes, eukaryotic microbes, such as yeast cultures,may also be used. Saccharomyces cerevisiae, or common baker's yeast, isthe most commonly used among eukaryotic microorganisms, although anumber of other strains are commonly available. For expression inSaccharomyces, the plasmid YRp7, for example (Stinchcomb et al., Nature282, 39 [1979]; Kingsman et al., Gene 7, 141 [1979]; Tschemper et al.,Gene 10, 157 [1980]), is commonly used. This plasmid already containsthe trp1 gene that provides a selection marker for a mutant strain ofyeast lacking the ability to grow in tryptophan, for example, ATCC No.44,076 or PEP4-1 (Jones, Genetics, 85, 12 [1977]). The presence of thetrp1 lesion as a characteristic of the yeast host cell genome thenprovides an effective environment for detecting transformation by growthin the absence of tryptophan.

Suitable promoting sequences in yeast vectors include the promoters for3-phosphoglycerate kinase (Hitzeman et al., J. Biol. Chem. 255, 2073[1980]) or other glycolytic enzymes (Hess et al., J. Adv. Enzyme Reg. 7,149 [1968]; Holland et al., Biochemistry 17, 4900 [1978]), such asenolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvatedecarboxylase, phospho-fructokinase, glucose-6-phosphate isomerase,3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase,phosphoglucose isomerase, and glucokinase. In constructing suitableexpression plasmids, the termination sequences associated with thesegenes are also ligated into the expression vector 3′ of the sequencedesired to be expressed to provide polyadenylation of the mRNA andtermination. Other promoters, which have the additional advantage oftranscription controlled by growth conditions, are the promoter regionfor alcohol dehydrogenase 2, isocytochrome C, acid phosphatase,degradative enzymes associated with nitrogen metabolism, and theaforementioned glyceraldehyde-3-phosphate dehydrogenase, and enzymesresponsible for maltose and galactose utilization. Any plasmid vectorcontaining yeast-compatible promoter, origin of replication andtermination sequences is suitable.

In addition to microorganisms, cultures of cells derived frommulticellular organisms may also be used as hosts. In principle, anysuch cell culture is workable, whether from vertebrate or invertebrateculture. However, interest has been greatest in vertebrate cells, andpropagation of vertebrate cells in culture (tissue culture) has become aroutine procedure in recent years [Tissue Culture, Academic Press, Kruseand Patterson, editors (1973)]. Examples of such useful host cell linesare VERO and HeLa cells, Chinese hamster ovary (CHO) cell lines, andW138, BHK, COS-7, 293, and MDCK cell lines. Expression vectors for suchcells ordinarily include (if necessary) an origin of replication, apromoter located in front of the gene to be expressed, along with anynecessary ribosome binding sites, RNA splice sites, polyadenylationsites, and transcriptional terminator sequences.

For use in mammalian cells, the control functions on the expressionvectors are often provided by viral material. For example, commonly usedpromoters are derived from polyoma, Adenovirus2, and most frequentlySimian Virus 40 (SV40). The early and late promoters of SV40 virus areparticularly useful because both are obtained easily from the virus as afragment that also contains the SV40 viral origin of replication [Fierset al., Nature, 273, 113 (1978)]. Smaller or larger SV40 fragments mayalso be used, provided there is included the approximately 250-bpsequence extending from the HindIII site toward the BgII site located inthe viral origin of replication. Further, it is also possible, and oftendesirable, to utilize promoter or control sequences normally associatedwith the desired gene sequence, provided such control sequences arecompatible with the host cell systems.

An origin of replication may be provided either by construction of thevector to include an exogenous origin, such as may be derived from SV40or other viral (e.g., Polyoma, Adeno, VSV, BPV) source, or may beprovided by the host cell chromosomal replication mechanism. If thevector is integrated into the host cell chromosome, the latter is oftensufficient.

Satisfactory amounts of protein are produced by cell cultures; however,refinements, using a secondary coding sequence, serve to enhanceproduction levels even further. One secondary coding sequence comprisesdihydrofolate reductase (DHFR) that is affected by an externallycontrolled parameter, such as methotrexate (MTX), thus permittingcontrol of expression by control of the methotrexate concentration.

In selecting a preferred host cell for transfection by the vectors ofthe invention 10 that comprise DNA sequences encoding both VEGF and DHFRprotein, it is appropriate to select the host according to the type ofDHFR protein employed. If wild-type DHFR protein is employed, it ispreferable to select a host cell that is deficient in DHFR, thuspermitting the use of the DHFR coding sequence as a marker forsuccessful transfection in selective medium that lacks hypoxanthine,glycine, and thymidine. An appropriate host cell in this case is theChinese hamster ovary (CHO) cell line deficient in DHFR activity,prepared and propagated as described by Urlaub and Chasin, Proc. Natl.Acad. Sci. (USA) 77, 4216 (1980).

On the other hand, if DHFR protein with low binding affinity for MTX isused as the controlling sequence, it is not necessary to useDHFR-deficient cells. Because the mutant DHFR is resistant tomethotrexate, MTX-containing media can be used as a means of selectionprovided that the host cells are themselves methotrexate sensitive. Mosteukaryotic cells that are capable of absorbing MTX appear to bemethotrexate sensitive. One such useful cell line is a CHO line, CHO-K1(ATCC No. CCL 61).

b. Typical Methodology Employable

Construction of suitable vectors containing the desired coding andcontrol sequences employs standard ligation techniques. Isolatedplasmids or DNA fragments are cleaved, tailored, and religated in theform desired to prepare the plasmids required.

If blunt ends are required, the preparation may be treated for 15minutes at 15° C. with 10 units of Polymerase I (Kienow),phenol-chloroform extracted, and ethanol precipitated.

Size separation of the cleaved fragments may be performed using 6percent polyacrylamide gel described by Goeddel et al., Nucleic AcidsRes. 8, 4057 (1980).

For analysis to confirm correct sequences in plasmids constructed, theligation mixtures are typically used to transform E. coli K12 strain 294(ATCC 31,446) or other suitable E. coli strains, and successfultransformants selected by ampicillin or tetracycline resistance whereappropriate. Plasmids from the transformants are prepared and analyzedby restriction mapping and/or DNA sequencing by the method of Messing etal., Nucleic Acids Res. 9, 309 (1981) or by the method of Maxam et al.,Methods of Enzymology 65, 499 (1980).

After introduction of the DNA into the mammalian cell host and selectionin medium for stable transfectants, amplification of DHFR-protein-codingsequences is effected by growing host cell cultures in the presence ofapproximately 20,000-500,000 nM concentrations of methotrexate, acompetitive inhibitor of DHFR activity. The effective range ofconcentration is highly dependent, of course, upon the nature of theDHFR gene and the characteristics of the host. Clearly, generallydefined upper and lower limits cannot be ascertained. Suitableconcentrations of other folic acid analogs or other compounds thatinhibit DHFR could also be used. MTX itself is, however, convenient,readily available, and effective.

Other techniques employable are described in a section just prior to theexamples.

4. Utilities and Formulation

The VEGF molecules herein have a number of therapeutic uses associatedwith the vascular endothelium. Such uses include the treatment oftraumata to the vascular network, in view of the demonstrated rapidpromotion by VEGF of the proliferation of vascular endothelial cellsthat would surround the traumata. Examples of such traumata that couldbe so treated include, but are not limited to, surgical incisions,particularly those involving the heart, wounds, including lacerations,incisions, and penetrations of blood vessels, and surface ulcersinvolving the vascular endothelium such as diabetic, haemophiliac, andvaricose ulcers. Other physiological conditions that could be improvedbased on the selective mitogenic character of VEGF are also includedherein.

For the traumatic indications referred to above, the VEGF molecule willbe formulated and dosed in a fashion consistent with good medicalpractice taking into account the specific disorder to be treated, thecondition of the individual patient, the site of delivery of the VEGF,the method of administration, and other factors known to practitioners.Thus, for purposes herein, the “therapeutically effective amount” of theVEGF is an amount that is effective either to prevent, lessen theworsening of, alleviate, or cure the treated condition, in particularthat amount which is sufficient to enhance the growth of vascularendothelium in vivo.

VEGF amino acid sequence variants and derivatives that areimmunologically crossreactive with antibodies raised against native VEGFare useful in immunoassays for VEGF as standards, or, when labeled, ascompetitive reagents.

The VEGF is prepared for storage or administration by mixing VEGF havingthe desired degree of purity with physiologically acceptable carriers,excipients, or stabilizers. Such materials are non-toxic to recipientsat the dosages and concentrations employed. If the VEGF is watersoluble, it may be formulated in a buffer such as phosphate or otherorganic acid salt preferably at a pH of about 7 to 8. If a VEGF variantis only partially soluble in water, it may be prepared as amicroemulsion by formulating it with a nonionic surfactant such asTween, Pluronics, or PEG, e.g., Tween 80, in an amount of 0.04-0.05%(w/v), to increase its solubility.

Optionally other ingredients may be added such as antioxidants, e.g.,ascorbic acid; low molecular weight (less than about ten residues)polypeptides, e.g., polyarginine or tripeptides; proteins, such as serumalbumin, gelatin, or immunoglobulins; hydrophilic polymers such aspolyvinylpyrrolidone; amino acids, such as glycine, glutamic acid,aspartic acid, or arginine; monosaccharides, disaccharides, and othercarbohydrates including cellulose or its derivatives, glucose, mannose,or dextrins; chelating agents such as EDTA; and sugar alcohols such asmannitol or sorbitol.

The VEGF to be used for therapeutic administration must be sterile.Sterility is readily accomplished by filtration through sterilefiltration membranes (e.g., 0.2 micron membranes). The VEGF ordinarilywill be stored in lyophilized form or as an aqueous solution if it ishighly stable to thermal and oxidative denaturation. The pH of the VEGFpreparations typically will be about from 6 to 8, although higher orlower pH values may also be appropriate in certain instances. It will beunderstood that use of certain of the foregoing excipients, carriers, orstabilizers will result in the formation of salts of the VEGF.

If the VEGF is to be used parenterally, therapeutic compositionscontaining the VEGF generally are placed into a container having asterile access port, for example, an intravenous solution bag or vialhaving a stopper pierceable by a hypodermic injection needle.

Generally, where the disorder permits, one should formulate and dose theVEGF for site-specific delivery. This is convenient in the case ofwounds and ulcers.

Sustained release formulations may also be prepared, and include theformation of microcapsular particles and implantable articles. Forpreparing sustained-release VEGF compositions, the VEGF is preferablyincorporated into a biodegradable matrix or microcapsule. A suitablematerial for this purpose is a polylactide, although other polymers ofpoly-(a-hydroxycarboxylic acids), such as poly-D-(−)-3-hydroxybutyricacid (EP 133,988A), can be used. Other biodegradable polymers includepoly(lactones), poly(acetals), poly(orthoesters), orpoly(orthocarbonates). The initial consideration here must be that thecarrier itself, or its degradation products, is nontoxic in the targettissue and will not further aggravate the condition. This can bedetermined by routine screening in animal models of the target disorderor, if such models are unavailable, in normal animals. Numerousscientific publications document such animal models.

For examples of sustained release compositions, see U.S. Pat. No.3,773,919, EP 58,481A, U.S. Pat. No. 3,887,699, EP 158,277A, CanadianPatent No. 1176565, U. Sidman et al., Biopolymers 22, 547 [1983], and R.Langer et al., Chem. Tech. 12, 98 [1982].

When applied topically, the VEGF is suitably combined with otheringredients, such as carriers and/or adjuvants. There are no limitationson the nature of such other ingredients, except that they must bepharmaceutically acceptable and efficacious for their intendedadministration, and cannot degrade the activity of the activeingredients of the composition. Examples of suitable vehicles includeointments, creams, gels, or suspensions, with or without purifiedcollagen. The compositions also may be impregnated into transdermalpatches, plasters, and bandages, preferably in liquid or semi-liquidform.

For obtaining a gel formulation, the VEGF formulated in a liquidcomposition may be mixed with an effective amount of a water-solublepolysaccharide or synthetic polymer such as polyethylene glycol to forma gel of the proper viscosity to be applied topically. Thepolysaccharide that may be used includes, for example, cellulosederivatives such as etherified cellulose derivatives, including alkylcelluloses, hydroxyalkyl celluloses, and alkylhydroxyalkyl celluloses,for example, methylcellulose, hydroxyethyl cellulose, carboxymethylcellulose, hydroxypropyl methylcellulose, and hydroxypropyl cellulose;starch and fractionated starch; agar; alginic acid and alginates; gumarabic; pullullan; agarose; carrageenan; dextrans; dextrins; fructans;inulin; mannans; xylans; arabinans; chitosans; glycogens; glucans; andsynthetic biopolymers; as well as gums such as xanthan gum; guar gum;locust bean gum; gum arabic; tragacanth gum; and karaya gum; andderivatives and mixtures thereof. The preferred gelling agent herein isone that is inert to biological systems, nontoxic, simple to prepare,and not too runny or viscous, and will not destabilize the VEGF heldwithin it.

Preferably the polysaccharide is an etherified cellulose derivative,more preferably one that is well defined, purified, and listed in USP,e.g., methylcellulose and the hydroxyalkyl cellulose derivatives, suchas hydroxypropyl cellulose, hydroxyethyl cellulose, and hydroxypropylmethylcellulose. Most preferred herein is methylcellulose.

The polyethylene glycol useful for gelling is typically a mixture of lowand high molecular weight polyethylene glycols to obtain the properviscosity. For example, a mixture of a polyethylene glycol of molecularweight 400-600 with one of molecular weight 1500 would be effective forthis purpose when mixed in the proper ratio to obtain a paste.

The term “water soluble” as applied to the polysaccharides andpolyethylene glycols is meant to include colloidal solutions anddispersions. In general, the solubility of the cellulose derivatives isdetermined by the degree of substitution of ether groups, and thestabilizing derivatives useful herein should have a sufficient quantityof such ether groups per anhydroglucose unit in the cellulose chain torender the derivatives water soluble. A degree of ether substitution ofat least 0.35 ether groups per anhydroglucose unit is generallysufficient. Additionally, the cellulose derivatives may be in the formof alkali metal salts, for example, the Li, Na, K, or Cs salts.

If methylcellulose is employed in the gel, preferably it comprises about2-5%, more preferably about 3%, of the gel and the VEGF is present in anamount of about 300-1000 mg per ml of gel.

The dosage to be employed is dependent upon the factors described above.As a general proposition, the VEGF is formulated and delivered to thetarget site or tissue at a dosage capable of establishing in the tissuea VEGF level greater than about 0.1 ng/cc up to a maximum dose that isefficacious but not unduly toxic. This intra-tissue concentration shouldbe maintained if possible by continuous infusion, sustained release,topical application, or injection at empirically determined frequencies.

It is within the scope hereof to combine the VEGF therapy with othernovel or conventional therapies (e.g., growth factors such as aFGF,bFGF, PDGF, IGF, NGF, anabolic steroids, EGF or TGF-a) for enhancing theactivity of any of the growth factors, including VEGF, in promoting cellproliferation and repair. It is not necessary that such cotreatmentdrugs be included per se in the compositions of this invention, althoughthis will be convenient where such drugs are proteinaceous. Suchadmixtures are suitably administered in the same manner and for the samepurposes as the VEGF used alone. The useful molar ratio of VEGF to suchsecondary growth factors is typically 1:0. 1-10, with about equimolaramounts being preferred.

5. Pharmaceutical Compositions

The compounds of the present invention can be formulated according toknown methods to prepare pharmaceutically useful compositions, wherebythe VEGF variants hereof is combined in admixture with apharmaceutically acceptable carrier vehicle. Suitable carrier vehiclesand their formulation, inclusive of other human proteins, e.g., humanserum albumin, are described, for example, in Remington's PharmaceuticalSciences, 16th ed., 1980, Mack Publishing Co., edited by Oslo et al. thedisclosure of which is hereby incorporated by reference. The VEGFvariants herein may be administered parenterally to subjects sufferingfrom cardiovascular diseases or conditions, or by other methods thatensure its delivery to the bloodstream in an effective form.

Compositions particularly well suited for the clinical administration ofVEGF variants hereof employed in the practice of the present inventioninclude, for example, sterile aqueous solutions, or sterile hydratablepowders such as lyophilized protein. It is generally desirable toinclude further in the formulation an appropriate amount of apharmaceutically acceptable salt, generally in an amount sufficient torender the formulation isotonic. A pH regulator such as arginine base,and phosphoric acid, are also typically included in sufficientquantities to maintain an appropriate pH, generally from 5.5 to 7.5.Moreover, for improvement of shelf-life or stability of aqueousformulations, it may also be desirable to include further agents such asglycerol. In this manner, variant t-PA formulations are renderedappropriate for parenteral administration, and, in particular,intravenous administration.

Dosages and desired drug concentrations of pharmaceutical compositionsof the present invention may vary depending on the particular useenvisioned. For example, in the treatment of deep vein thrombosis orperipheral vascular disease, “bolus” doses, will typically be preferredwith subsequent administrations being given to maintain an approximatelyconstant blood level, preferably on the order of about 3 μg/ml.

However, for use in connection with emergency medical care facilitieswhere infusion capability is generally not available and due to thegenerally critical nature of the underlying disease (e.g., embolism,infarct), it will generally be desirable to provide somewhat largerinitial doses, such as an intravenous bolus.

For the various therapeutic indications referred to for the compoundshereof, the VEGF molecules will be formulated and dosed in a fashionconsistent with good medical practice taking into account the specificdisorder to be treated, the condition of the individual patient, thesite of delivery, the method of administration and other factors knownto practitioners in the respective art.

Thus, for purposes herein, the “therapeutically effective amount” of theVEGF molecules hereof is an amount that is effective either to prevent,lessen the worsening of, alleviate, or cure the treated condition, inparticular that amount which is sufficient to enhance the growth ofvascular endothelium in vivo. In general a dosage is employed capable ofestablishing in the tissue that is the target for the therapeuticindication being treated a level of a VEGF mutant hereof greater thanabout 0.1 ng/cm³ up to a maximum dose that is efficacious but not undulytoxic. It is contemplated that intra-tissue administration may be thechoice for certain of the therapeutic indications for the compoundshereof.

The following examples are intended merely to illustrate the best modenow known for practicing the invention but the invention is not to beconsidered as limited to the details of such examples.

EXAMPLE I

Materials—Muta-gene phagemid in vitro mutagenesis kit, horse-radishperoxidase conjugated goat IgG specific for murine IgG, pre-stainedlow-range MW standards and Trans-Blot Transfer Medium (purenitrocellulose membrane) were purchased from BioRad Laboratories(Richmond, Calif.). Qiagen plasmid Tip 100 kit and Sequenase version 2.0were from Qiagen (Chatsworth, Calif.) and United States Biochemical(Cleveland, Ohio), respectively. SDS gels (4-20% gradientpolyacrylamide) and pre-cut blotting paper were from IntegratedSeparations Systems (Natick, Mass.). SDS sample buffer (5× concentrate)and various restriction enzymes were from New England Biolabs (Beverly,Mass.). O-phenylenediamine, citrate phosphate buffers, sodium dodecylsulfate, and H₂O₂ substrate tablets were purchased from Sigma (St.Louis, Mo.). BufferEZE formula 1 (transfer buffer) and X-OMat AR X-rayfilm were from Eastman Kodak Co. (Rochester, N.Y.). Maxosorb andImmunlon-1 microtiter plates were purchased from Nunc (Kamstrup,Denmark) and Dynatech (Chantilly, Va.), respectively. Cell cultureplates (12-well) and culture media (with calf serum) were from Costar(Cambridge, Mass.) and Gibco (Grand Island, N.Y.), respectively.Polyethylene-20-sorbitan monolaurate (Tween-20) was from Fisher Biotech(Fair Lawn, N.J.). G25 Sephadex columns (PD-10) and ₁₂₅I labeled ProteinA were from Pharmacia (Piscataway, N.J.) and Amersham (ArlingtonHeights, Ill.), respectively. Bovine serum albumin (BSA) and rabbit IgGanti-human IgG (Fc-specific) were purchased from Cappel (Durham, N.C.)and Calbiochem (La Jolla, Calif.), respectively. Plasmid vector (pRK5),competent E. coli cells (DH5a and CJ236), synthetic oligonucleotides,cell culture medium, purified CHO-derived VEGF₁₆₅, monoclonal (MatesA4.6.1, 2E3, 4D7, SC3, and SF8) and polyclonal antibodies to VEGF₁₆₅were prepared at Genentech, Inc. (South San Francisco, Calif.).Construction, expression and purification of FLT-1, flkl and KDRreceptor-IgG chimeras was as described by Park, etal. J. Biol. Chem.269, 25646-25654 (1994).

Site-directed Mutagenesis and Expression of VEGF Variants—Site-directedmutagenesis was performed using the Muta-Gene Phagemid in vitromutagenesis kit according to the method of Kunkel Proc. Natl. Acad. Sci.82, 488-492 (1985) and Kunkel etal., Methods Enzymol. 154, 367-382(1987). A plasmid vector pRK5 containing cDNA for VEGF₁₆₅ isoform wasused for mutagenesis and transient expression. The pRK5 vector is amodified pUC118 vector and contains a CMV enhancer and promoter[Nakamaye et al., Nucleic Acids Res. 14, 9679-9698 (1986) and Vieira etal, Methods Enzymol. 155, 3-11 (1987)]. The mutagenized DNA was purifiedusing the Qiagen Plasmid Midi Kit Tip 100 and the sequence of themutations was verified using Sequenase Version 2.0 Kit. The mutated DNAwas analyzed by restriction enzyme digestion as described by Sambrook,et al, Molecular Cloning: A Laboratory Manual part I, C5.28-5.32, ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989).

Transient transfection of human fetal kidney “293 cells” was performedin 6-well plates using the modified calcium phosphate precipitate methodas previously described [Jordan et al., Bio/Technology (manuscript inpreparation) (1994); Chen et al., Mol. Cell. Biol. 7, 2745-2752 (1987);Gorman et al., DNA and Protein Engineering Techniques 2, 3-10 (1990);Graham et al., Virology 52, 456-467 (1973)]. Briefly, approximately1.2×10⁶ cells were incubated overnight at 37° C. in the presence of 15μg of precipitated DNA. Cell culture supernatant was replaced with serumfree medium, and cell monolayers were incubated for 72 hours at 37° C.Conditioned media (3 ml) was harvested, centrifuged, aliquoted andstored at −70° C. until use.

Quantitation of VEGF₁₆₅ Variants by ELISA—A radioimmunometric assaypreviously described [Aiello et al., N. Engl. J. Med. 331, 1480-1487(1994)], was adapted for the quantitation of VEGF mutants by thefollowing procedure. Individual wells of a 96-well microtiter plate werecoated with 100 μl of a 3 μg/ml solution of an anti-VEGF₁₆₅ polyclonalantibody in 50 mM sodium carbonate buffer pH 9.6 overnight at 4° C. Thesupernatant was discarded, and the wells were washed 4 times with PBScontaining 0.03% Tween 80. The plate was blocked in assay buffer (0.5%BSA, 0.03% Tween 80, 0.01 % Thimerosal in PBS) for one hr (300 μl/well)at ambient temperature, then the wells were washed. Diluted samples (100μl) and VEGF₁₆₅ standard (ranging from 0.1 to 1 ng/ml) were added toeach well and incubated for one hr at ambient temperature with gentleagitation. The supernatant was discarded, and the wells were washed.Anti-VEGF murine monoclonal antibody 5F8 solution (100 μl at 1 μg/ml)was added, and the microtiter plate was incubated at ambient temperaturefor one hr with gentle agitation. After the supernatant was discarded,the plate was washed and horseradish peroxidase conjugated goat IgGspecific for murine IgG (100 μl) at a dilution of 1:25000 wasimmediately added to each well. The plate was incubated for one hr atambient temperature with gentle agitation after which the supernatantdiscarded, the wells washed, and developed by addition oforthophenylenediamine (0-04%), H₂O₂ (0.012%) in 50 mM citrate phosphatebuffer pH 5 (100 μl), then incubated in the dark at ambient temperaturefor 10 min. The reaction was stopped by adding 50 μl of 4.5 N H₂SO₄ toeach well and the absorbance was measured at 492 nm on a microplatereader (SLT Labs). The concentrations of VEGF₁₆₅ variants werequantitated by interpolation of a standard curve using non-linearregression analysis. For purposes of comparison, a second ELISA wasdeveloped that utilized a dual monoclonal format. The assay was similarto the above described ELISA, except a neutralizing monoclonal antibody(Mab A4.6.1) was used to coat the microtiter plates [Kim et al., GrowthFactors 7, 53-64 (1992)].

Immunoblotting of VEGF mutants—Aliquots of conditioned cell media (16μl) containing VEGF or VEGF mutant (approx. 10 ng) were added to 5×SDSsample buffer (4 μl) and heated at 90° C. for 3 min prior to loading onSDS polyacrylamide (4 to 20% acrylamide) gels. Pre-stained MW standards(10 μl) were loaded in the outer lanes of the SDS gels. Gels were run at25 mA for 90 min at 4° C. Gels were transferred to nitrocellulose paperin a Bio-Rad tank blotter containing BufferEZE with 0.1% SDS for 90 minat 250 mA at 25° C. Nitrocellulose was pre-wetted in transfer bufferwith 0.1 % SDS for 10 min prior to use. Transferred immunoblots wereblocked in PBS overnight with 1.0% BSA and 0.1% Tween 20 (blockingbuffer) at 4° C. A solution containing 5 murine anti-VEGF Mabs (A.4.6.1,5C3, 5F8, 4D7, and 2E3) was prepared with 2 μg/ml of each Mab inblocking buffer and used as primary antibody. The primary antibodysolution was incubated with the immunoblots for 4 hr at 25° C. withgentle agitation, then washed 3× for 10 min in blocking buffer at 25° C.¹²⁵I labeled Protein A was diluted to 10⁴ cpm/ml (final concentration)in blocking buffer and incubated with the immunoblots for 60 min withgentle agitation at 25° C. Immunoblots were washed 3× for 10 min inblocking buffer at 25° C., then dried on filter paper and placed onKodak X-Omat film with two intensifying screens at −70° C. for 3 days.

Preparation of ¹²⁵I labeled VEGF₁₆₅—Radiolabeling of CHO-derived VEGF₁₆₅was prepared using a modification of the chloramine T catalyzediodination method [Hunter et al., Nature 194, 495-496 (1962)]. In atypical reaction, 10 μl of 1 M Tris-HCl, 0.01% Tween 20 at pH 7.5 wasadded to 5 μl of sodium iodide-125 (0.5 milliCuries, 0.24 nmol) in acapped reaction vessel. To this reaction, 10 μl of CHO-derived VEGF₁₆₅(10 μg, 0.26 nmol) was added. The iodination was initiated by additionof 10 μl of 1 mg/ml chloramine T in 0.1 M sodium phosphate, pH 7.4.After 60 sec, iodination was terminated by addition of sodiummetabisulfite (20 μl, 1 mg/ml) in 0.1 M sodium phosphate, pH 7.5. Thereaction vessel was vortexed after each addition. The reaction mixturewas applied to a PD-10 column (G25 Sephadex) that was pre-equilibratedwith 0.5% BSA, 0.01 % Tween 20 in PBS. Fractions were collected andcounted for radioactivity with a gamma scintillation counter (LKB model1277). Typically, the specific radioactivity of the iodinated VEGF was26±2.5 μCi/μg, which corresponded to one ¹²⁵I per two molecules ofVEGF₁₆₅ dimer.

VEGF₁₆₅ Receptor Binding Assay—The assay was performed in 96-wellimmunoplates (Immulon-1); each well was coated with 100 μl of a solutioncontaining 10 μg/ml of rabbit IgG anti-human IgG (Fc-specific) in 50 mMsodium carbonate buffer pH 9.6 overnight at 4° C. After the supernatantwas discarded, the wells were washed three times in washing buffer(0.01% Tween 80 in PBS). The plate was blocked (300 μl/well) for one hrin assay buffer (0.5% BSA, 0.03% Tween 80, 0.01% Thimerosal in PBS). Thesupernatant was discarded and the wells were washed. A cocktail wasprepared with conditioned cell media containing VEGF₁₆₅ mutants atvarying concentrations (100 μl), ¹²⁵I radiolabeled VEGF₁₆₅ (approx.5×10₃ cpm in 50 μl) which was mixed with VEGF receptor-IgG chimericprotein, FLT-1 IgG, flk-1 IgG or KDR-IgG (3-15 ng/ml, finalconcentration, 50 μl) in micronic tubes. Aliquots of this solution (100μl) were added to pre-coated microtiter plates and incubated for 4 hr atambient temperature with gentle agitation. The supernatant wasdiscarded, the plate washed, and individual microtiter wells werecounted by gamma scintigraphy (LKB model 1277). The competitive bindingbetween unlabeled VEGF₁₆₅ (or VEGF₁₆₅ mutants) and ¹²⁵I radiolabeledVEGF₁₆₅ to the FLT-1, Flk-1, or KDR receptors were plotted, and analyzedusing a four parameter fitting program (Kaleidagraph, AdelbeckSoftware). The apparent dissociation constant for each VEGF mutant wasestimated from the concentration required to achieve 50% inhibition(IC₅₀).

Assay for Vascular Endothelial Cell Growth—The mitogenic activity of 30VEGF variants was determined by using bovine adrenal corticalendothelial (ACE) cells as target cells as previously described [Ferraraet al., Biochem. Biophys. Res. Comm. 161, 851-859 (1989)]. Briefly,cells were plated sparsely (7000 cells/well) in 12 well plates andincubated overnight in Dulbecco's modified Eagle's medium supplementedwith 10% calf serum, 2 mM glutamine, and antibiotics. The medium wasexchanged the next day, and VEGF or VEGF mutants, diluted in culturemedia at concentrations ranging from 100 ng/ml to 10 pg/ml, were layeredin duplicate onto the seeded cells. After incubation for 5 days at 37°C., the cells were dissociated with trypsin, and quantified using aCoulter counter.

Isolation of VEGF cDNA

Total RNA was extracted [Ullrich et al., Science 196, 1313-1317 (1977)]from bovine pituitary follicular cells [obtained as described by Ferraraet al., Meth. Enzymol. supra, and Ferrara et al., Am. J. Physiol.,supra] and the polyadenylated mRNA fraction was isolated byoligo(dT)-cellulose chromatography. Aviv et al., Proc. Natl. Acad. Sci.USA 69, 1408-1412 (1972). The cDNA was prepared [Wickens et al., J.Biol. Chem. 253, 2483-2495 (1978)] by priming with dT₁₂-₁₈ or a randomhexamer dN₆. The double-stranded cDNA was synthesized using a cDNA kitfrom Amersham, and the resulting cDNA was subcloned into EcoRI-cleavedIgt10 as described [Huynh et al., DNA Cloning Techniques, A PracticalApproach, Glover ed. (IRL, Oxford, 1985)], except that asymmetric EcoRIlinkers [Norris et al., Gene 7, 355-362 (1979)] were used, thus avoidingthe need for the EcoRI methylase treatment.

The recombinant phage were plated on E. coli C600 Hfl [Huynh et al.supra] and replica plated onto nitrocellulose filters. Benton et al.,Science 196, 180-182 (1977). These replica were hybridized with a³²P-labeled [Taylor et al., Biochim. Biophys. Acta, 442, 324-330 (1976)]synthetic oligonucleotide probe of the sequence:5′-CCTATGGCTGAAGGCGGCCAGAAGCCTCACGAAGTGGTGAAGTTCATGGACGTGTATCA-3′ at 42°C. in 20% formamide, 5×SSC, 50 mM sodium phosphate pH 6.8, 0.1% sodiumpyrophosphate, 5× Denhardt's solution, and 50 mg/ml salmon sperm DNA,and washed in 2×SSC, 0.1% SDS at 42° C.

One positive clone, designated i.vegf.6, was identified. This clone,labeled with ³²P, was used as a probe to screen an oligo-dT-primed humanplacenta cDNA library, and positive clones were observed. When a humanpituitary cDNA library was screened with the same labeled clone, nopositive clones were detected.

The complete nucleotide sequence of the clone I.vegf.6 was determined bythe dideoxyoligonucleotide chain termination method [Sanger et al.,Proc. Natl. Acad. Sci. USA 74, 5463-5467 (1977)] after subcloning intothe pRK5 vector. The sequence obtained, along with the imputed aminoacid sequence, including the signal sequence.

Expression of VEGF-Encoding Gene in Mammalian Cells

The final expression vector, pRK5.vegf.6, was constructed from I.vegf.6and pRK5. The construction of pRK5 and pRK5.vegf.6 is described below indetail.

A. Construction of pRK5 A.1. Construction of pF8CIS

The initial three-part construction of the starting plasmid pF8CIS isdescribed below.

-   1) The ampicillin resistance marker and replication origin of the    final vector was derived from the starting plasmid pUC13pML, a    variant of the plasmid pML (Lusky, M. and Botchen, M., Nature, 293,    79 [1981]). pUC13pML was constructed by transferring the polylinker    of pUC13 (Vieira, J. and Messing, J., Gene, 19, 259 (1982) to the    EcoRI and HindIII sites of pML. A second starting plasmid pUC8-CMV    was the source of the CMV enhancer, promoter and splice donor    sequence. pUC8-CMV was constructed by inserting approximately 800    nucleotides for the CMV enhancer, promoter and splice donor sequence    into the blunted PstI and SphI sites of pUC8. Vieira, J. and    Messing, J., op. cit. Synthetic BamHI-HindIII linkers (commercially    available from New England Biolabs) were ligated to the cohesive    BamHI end creating a HindIII site. Following this ligation a    HindIII-HincII digest was performed. This digest yielded a fragment    of approximately 800 bp that contained the CMV enhancer, promoter    and splice donor site. Following gel isolation, this 800 bp fragment    was ligated to a 2900 bp piece of pUC13pML. The fragment required    for the construction of pF8CIS was obtained by digestion of the    above intermediate plasmid with SalI and HindIII. This 3123 bp piece    contained the resistance marker for ampicillin, the origin of    replication from pUC13pML, and the control sequences for the CMV,    including the enhancer, promoter, and splice donor site.

2) The Ig variable region intron and splice acceptor sequence wasconstructed using a synthetic oligomer. A 99 mer and a 30 mer werechemically synthesized having the following sequence for the IgG intronand splice acceptor site (Bothwell et al., Nature, 290, 65-67 [1981]): 1 5′ AGTAGCAAGCTTGACGTGTGGCAGGCTTGA... 31   GATCTGGCCATACACTTGAGTGACAATGA... 60   CATCCACTTTGCCTTTCTCTCCACAGGT... 88    GTCCACTCCCAG 3′  13′ CAGGTGAGGGTGCAGCTTGACGTCGTCGGA 5′

-    DNA polymerase I (Klenow fragment) filled in the synthetic piece    and created a double-stranded fragment. Wartell, R. M. and W. S.    Reznikoff, Gene, 9, 307 (1980). This was followed by a double digest    of PstI and HindIII. This synthetic linker was cloned into pUC13    (Veira and Messing, op. cit.) at the PstI and HindIII sites. The    clones containing the synthetic oligonucleotide, labeled pUCIg.10,    was digested with PstI. A ClaI site was added to this fragment by    use of a PstI-ClaI linker. Following digestion with HindIII a 118-bp    piece containing part of the Ig intron and the Ig variable region    splice acceptor was gel isolated.-   3) The third part of the construction scheme replaced the hepatitis    surface antigen 3′ end with the polyadenylation site and    transcription termination site of the early region of SV40. A    vector, pUC.SV40, containing the SV40 sequences was inserted into    pUC8 at the BamHI site described by Vieira and Messing, op. cit.    pUC.SV40 was then digested with EcoRI and HpaI. A 143bp fragment    containing the SV40 polyadenylation sequence was gel isolated from    this digest. Two additional fragments were gel isolated following    digestion of pSVE.8c1D. (European Pat. Pub. No. 160,457). The 4.8 kb    fragment generated by EcoRI and Cla1 digestion contains the    SV40-DHFR transcription unit, the origin of replication of pML and    the ampicillin resistance marker. The 7.5-kb fragment produced    following digestion with ClaI and HpaI contains the cDNA for    Factor VIII. A three-part ligation yielded pSVE.8c24D. This    intermediate plasmid was digested by ClaI and SalI to give a 9611 bp    fragment containing the cDNA for Factor VIII with an SV40 poly A    site followed by the SV40 DHFR transcription unit.

The final three-part ligation to yield pF8CIS used: a) the 3123 bpSalI-HindIII fragment containing the origin of replication, theampicillin resistance marker, and the CMV enhancer, promoter, and splicedonor site; b) the 118 bp HindIII-ClaI fragment containing the Ig intronand splice acceptor site; and c) a 9611 bp ClaI-SalI fragment containingthe cDNA for Factor VIII, the SV40 polyadenylation site, and the SV40DHFR transcription unit.

A.2. Construction of pCIS2.8c28D

pCIS2.8c28D comprises a 90 kd subunit of Factor VIII joined to a 73 kdsubunit of Factor VIII. The 90 kd comprises amino acids 1 through 740and the 73 kd subunit amino acids 1690 through 2332. This construct wasprepared by a three-part ligation of the following fragments: a) the12617-bp ClaI-SstII fragment of pF8CIS (isolated from a dam-strain andBAP treated); b) the 216-bp SstII-PstI fragment of pF8CIS; and c) ashort PstI-ClaI synthetic oligonucleotide that was kinased.

FIG. 4 also shows the subcloning of the 408 bp BamHI-HindIII and the 416bp BamHI-PstI fragments of pSVEFVIIII (European Pat. Publ. No. 160,457)containing the 5′ and 3′ DNA regions of Factor VIII to be fused to makepCIS2.8c28D.

FIG. 5 shows the three-part ligation used to construct the fusion regionof pCIS2.8c28D. Two different fragments, A and B, were cloned into thesame pUC118 BamHI-PstI BAP vector. The A fragment was the 408 bpBamHI-HindIII fragment of pUC408BH and the B fragment was a HindIII-PstIoligonucleotide. This oligonucleotide was used without kinasing toprevent its polymerization during ligation.

After ligation of the A and B fragments into the vector, the expectedjunction sequences were confirmed by DNA sequencing of the regionsencompassed by the nucleotides.

The resulting plasmid, pCIS2.8c28D, was constructed with a four-partligation. The fusion plasmid was cut with BamHI and PstI and the 443 bpfragment isolated. The remaining three fragments of the four-partligation were: 1) 1944 bp ClaI-BamHI of pSVEFVIII (European Pat. Publ.No. 160,457); 2) a 2202 bp BamHI-XbaI fragment of pSVEFVIII, which wasfurther partially digested with PstI and the 1786 bp PstI-XbaI fragmentwas isolated, and 3) the 5828 bp XbaI-ClaI BAP fragment of pCIS2.8c24D.The translated DNA sequence of the resultant variant in the exact fusionjunction region of pCIS2.8c28D was determined and correlates.

A.3. Construction of pRK5

The starting plasmid for construction of pRK5 was pCIS2.8c28D. The basenumbers in paragraphs 1 through 6 refer to pCIS2.8c28D with base one ofthe first T of the EcoRI site preceding the CMV promoter. Thecytomegalovirus early promoter and intron and the SV40 origin and polyAsignal were placed on separate plasmids.

-   1. The cytomegalovirus early promoter was cloned as an EcoRI    fragment from pCIS2.8c28D (9999-1201) into the EcoRI site of pUC118    described above. Twelve colonies were picked and screened for the    orientation in which single-stranded DNA made from pUC118 would    allow for the sequencing from the EcoRI site at 1201 to the EcoRI    site at 9999. This clone was named pCMVE/P.-   2. Single-stranded DNA was made from pCMVE/P in order to insert an    SP6 (Green, M R et al., Cell 32, 681-694 [1983]) promoter by    site-directed mutagenesis. A synthetic 110 mer that contained the    sequences from −69 to +5 of SP6 promoter (see Nucleic Acids Res.,    12, 7041 [1984]) were used along with 18-bp fragments on either end    of the oligomer corresponding to the CMVE/P sequences. Mutagenesis    was done by standard techniques and screened using a labeled 110 mer    at high and low stringency. Six potential clones were selected and    sequenced. A positive clone was identified and labeled pCMVE/PSP6.-   3. The SP6 promoter was checked and shown to be active, for example,    by adding SP6 RNA polymerase and checking for RNA of the appropriate    size.-   4. A Cla-NotI-Sma adapter was synthesized to encompass the location    from the ClaI site (912) to the SmaI site of pUC118 in pCMVE/P    (step 1) and pCMVE/PSP6 (step 2). This adapter was ligated into the    ClaI-SmaI site of pUC118 and screened for the correct clones. The    linker was sequenced in both and clones were labeled pCMVE/PSP6-L    and pCMVE/P-L.-   5. pCMVE/PSP6-L was cut with SmaI (at linker/pUC118 junction) and    HindIII (in pUC118). A Hpai (5573)-to-HindIII (6136) fragment from    pSVORAADRI 11, described below, was inserted into SmaI-HindIII of    pCMVE/PSP6-L. This ligation was screened and a clone was isolated    and named pCMVE/PSP6-L-SVORAADRI.    -   a) The SV40 origin and polyA signal was isolated as the        Xmnl (5475) -HindIII (6136) fragment from pCIS2.8c28D and cloned        into the HindIII to SmaI sites of pUC119 (described in Vieira        and Messing, op. cit.). This clone was named pSVORAA.    -   b) The EcoRI site at 5716 was removed by partial digestion with        EcoRI and filling in with Klenow. The colonies obtained from        self-ligation after fill-in were screened and the correct clone        was isolated and named pSVORAADRI 11. The deleted EcoRI site was        checked by sequencing and shown to be correct.    -   c) The Hpal (5573) to HindIII (6136) fragment of pSVORAADRI 11        was isolated and inserted into pCMVE/PSP6-L (see 4 above).-   6. pCMVE/PSP6-L-SVOrAADRI (step 5) was cut with EcoRI at 9999,    blunted and self-ligated. A clone without an EcoRI site was    identified and named pRK.-   7. pRK was cut with SmaI and BamHI. This was filled in with Kienow    and relegated. The colonies were screened. A positive clone was    identified and named pRKDBam/Sma3.-   8. The HindIII site of pRKDBam/Sma3 was converted to a HpaI site    using a converter. (A converter is a piece of DNA used to change one    restriction site to another. In this case one end would be    complementary to a HindIII sticky end and the other end would have a    recognition site for HpaI.) A positive clone was identified and    named pRKDBam/Sma, HIII-HpaI 1.-   9. pRKDBam/Sma, HII-HpaI 1 was cut with PstI and NotI and an    EcoRI-HindIII linker and HindIII-EcoRI linker were ligated in.    Clones for each linker were found. However, it was also determined    that too many of the Hpal converters had gone in (two or more    converters generate a PvuII site). Therefore, these clones had to be    cut with HpaI and self-ligated.-   10. RI-HIII clone 3 and HIII-RI clone 5 were cut with HpaI, diluted,    and self-ligated. Positives were identified. The RI-HIII clone was    named pRK5.

B. Construction of pRK5.vegf.6

The clone I.vegf.6 was treated with EcoRI and the EcoRI insert wasisolated and ligated into the vector fragment of pRK5 obtained bydigestion of pRK5 with EcoRI and isolation of the large fragment. Thetwo-part ligation of these fragments yielded the expression vector,pRK5.vegf.6, which was screened for the correct orientation of theVEGF-encoding sequence with respect to the promoter.

Further details concerning the construction of the basic pRK5 vector canbe taken from U.S. Pat. No. 5,332,671 that issued on 26 Jul. 1994.

EXAMPLE 2

The following example details the methodology generally employed toprepare the various mutants covered by the present invention. The basicexpression vector was prepared as follows:

Vector SDVF₁₆₅ containing the cDNA of VEGF₁₆₅ was obtained and isdepicted in FIG. 13 herein. The cDNA for VEGF₁₆₅ was isolated fromSDVF₁₆₅ by restriction digestion with Hind III and Eco RI. This isolatedinsert was ligated into the pRK5 plasmid taking advantage to theexistence therein of Eco RI and Hind III sites—see the construct asdepicted in FIG. 14 hereof. The resultant plasmid was transformed intocompetent CJ236 E. coli cells to make a template for site-directedmutagenesis. The corresponding oligonucleotide containing the mutatedsite was then prepared—see infra—and the in vitro site-directedmutagenesis step was conducted in accordance with known procedures usingthe BioRad Muta-Gene mutagenesis kit. After sequencing to determine thatthe mutagenesized site was incorporated into the final expressionvector, the resultant vector was transfected into 293 human kidney cellsfor transient expression. Reference is made to FIG. 15 which provides ageneral depiction of the construction of such expression vectors.

The following oligonucleotides were prepared in order to make the finalmutated product. Table 2 provides such information. TABLE 2 MUTATION5′-----------3′ SEQUENCE E5A CCCTCCTCCGGCTGCCATGGGTGC H11A, H12A,CTTCACCACGGCGGCGGCATTCTGCCCTCC E13A K16A, D19ACTGATAGACGGCCATGAAGGCCACCACTTCGTG R23A GCAGTAGCTGGCCTGATAGACATC H27A,E30A CACCAGGGTGGCGATTGGGGCGCAGTAGCTGCG D34A, E38AATCAGGGTAGGCCTGGAAGATGGCCACCAGGGTCTC D41A, E42A,GAAGATGTAGGCGATGGCGGCAGGGTACTCCTG E44A K48A ACAGGATGGGGCGAAGATGTACTCR56A GCCCCCGCAGGCCATCAGGGGCAC D63, AE64,GGGCACACAGGCCAGGCCGGCGGCATTGCAGCAGCC AE67A E72A, E73AGATGTTGGAGGCGGCAGTGGGCACACA R82A, K84A,CTGGCCTTGGGCAGGGGCGATGGCCATAATCTGCAT H86A H90A, E93AGAAGCTCATGGCTCCTATGGCCTGGCCTTGGTG H99A, K101AGCATTCACAGGCGTTGGCCTGTAGGAAGCT E103A TGGTCTGCAGGCACATTTGTTGTG K107A,K108A, TTGTCTTGCGGCGGCGGCGGCTGGTCTGCATTC D109A, R110A K107A, K108ATGCTCTATCGGCGGCTGGTCTGCATTC D109A, R110A TTGTCTTGCGGCGGCTTTCTTTGGTCTR105A TTTCTTTGGGGCGCATTCACATTT R112A, E114AACAGGGATTGGCTTGGGCTGCTCTATCTTT N75A CATGGTGATGGCGGACTCCTCAGT H12TCACCACTTCGGTATGATTCTGCCC E64T CTCCAGGCCGGTGTCATTGCAGCA D143TGCAACGCGAGGTTGTGTTTTTGCA R156T TCTGCAAGTGGTTTCGTTTAACTC H11ACACCACTTCGTGGGCATTCTGCCCTCC H12A CTTCACCACTTCGGCATGATTCTGCCC E13AGAACTTCACCACGGCGTGATGATTCTG K16A GACATCCATGAAGGCCACCACTTCGTG D19AGCGCTGATAGACGGCCATGAACTTCACCAC H27A GGTCTCGATTGGGGCGCAGTAGCTGCG D34ACTCCTGGAAGATGGCCACCAGGGTCTC E38A CTCATCAGGGTAGGCCTGGAAGATGTC D41AGTAATCGATCTCGGCAGGGTACTCCTG E30A GTCCACCAGGGTGGCGATTGGATGGCA E42AGATGTACTCGATGGCATCAGGGTACTC E44A CTTGAAGATGTAGGCGATCTCATCCAG

Thus prepared in accordance with the insertion of the oligonucleotidesset forth in Table 2 above, left column there are prepared at thecorresponding mutation in the VEGF molecule in accordance with thenotation given under the left hand column entitled “Mutation”. Thenaming of the compound is in accord with naming convention. Thus, forthe first entry the mutation is referred to as “E5A”. This means that atthe 5 position of the VEGF molecule the glutamic acid (E) was mutated soas to insert an alanine (A) at that 5 position.

In accordance with the foregoing the following mutations were alsoinserted into the VEGF molecule. TABLE 3 MUTATIONS N62A G65A L66A M78AQ79A I80A M81A I83A P85A Q87A G88A Q89A I91A G92A H27A D63K E64R E67KD63K, E64R, E67K R82E K84E H86E R82E, K84E, H86E

The effects of such site-directed mutations in the VEGF molecule are setforth in Tables 4 and 5 hereof: TABLE 4 Half-Maximal EffectiveHalf-Maximal Concentration Variants Inhibitory (ng/ml) of Human VEGFConcentration (ng/ml) Endothelial Mean Mutation KDR-IgG FLT-IgG Cells 63D63A 0.18 1.54 2.47 64 E64A 8.0 0.94 1.65 64 E64S 1.90 6.25   64.7 D63A,E64A, 2.8 44.6 1.05 E67A 65 E64N, L66S 35.6 2.70 67 E67A 0.61 0.47 1.9982 R82A 0.87 1.23 1.95 83 RIK(82-84)NLS >10000 1.63 >100 84 K84A 6.31.91 2.00 84 R82A, K84A, 1340 1.70 19.8 H86A 86 H86A 2.0 1.19 1.75 WTVEGF (CHO cell) 1.32 0.95 0.54 WT VEGF (293 cell) 1.14 1.08Mean residue numberBoldface sequence indicates mutations that potentially alter VEGFglycosylation

TABLE 5 Half-Maximal Effective Half-Maximal Concentration VariantsInhibitory (ng/ml) of Human VEGF Concentration (ng/ml) Endothelial MeanMutation KDR-IgG FLT-IgG Cells  5 E5A 0.88 12 H11A, H12A, 1.2 0.62 2.55E13A   17.5 K16A, D19T 2.1 0.73 2.05 23 R23A 2.0 1.0 2.40 27 H27A na.na. na. 30 E30A 0.92 34 D34A 0.54 0.59 1.23 38 E38A 0.41 0.87 0.95 41D41A 0.65 42 E42A 0.26 0.51 0.77 43 E42N, E44S 0.59 0.77 1.00 44 E44A0.17 0.54 0.49 48 K48A 0.77 1.08 1.09 56 R56A na. na. na.   72.5 E72A,E73A 1.3 0.91 1.75 75 N75A 1.26 0.44   91.5 H90A, E93A 1.3 .077 1.28100  H99A, K101A 1.26 1.33 1.25 103  E103A 2.34 0.74 1.25 105  R105A1.63 1.57 3.20  107.5 K107A, K108A 2.99 2.94 0.95  108.5 KKDR(107- 2.942.42 1.00 110)AAAA  109.5 D109A, R110A 1.17 1.42 113  R112A, E114A 1.520.56 1.10 WT VEGF (CHO cell) 1.32 0.95 0.54 WT VEGE (293 cell) 1.14 1.08Mean residue numberBoldface sequence indicates mutations that potentially alter VEGFglycosylationThe data presented supra in Tables 4 and 5 may also be expressed as pMhalf-maximal inhibitory concentration and pM half-maximal effectiveconcentration as set forth in Table 6:

TABLE 6 Effects of Site-Directed Mutations in VEGF Half-MaximalEffective Half-Maximal Concentration Variants Inhibitory¹ (pM) of HumanVEGF Concentration (pM) Endothelial Mean² Mutation³ KDR-IgG FLT-IgGCells  5 E5A 37 ± 1 22 ± 1 23 ± 2 12 H11A, H12A, E13A 31 ± 2 20 ± 1 61 ±6   17.5 K16A, D19T 26 ± 3 19 ± 1  53 ± 14 23 R23A 51 ± 1 30 ± 2 63 ± 527 H27A n.a. n.a. n.a. 30 E30A 29 ± 1 28 ± 1 24 ± 1 34 D34A 14 ± 4 11 ±2 30 ± 1 38 E38A 11 ± 1 15 ± 2 29 ± 8 41 D41A 36 ± 1 22 ± 1 17 ± 1 42E42A  7 ± 1  8 ± 1 20 ± 3 43 E42N, E44S 15 ± 1 13 ± 1  27 ± 14 44 E44A 4 ± 1  9 ± 1 13 ± 1 48 K48A  20 ± 10 26 ± 1 29 ± 6 56 R56A n.a. n.a.n.a. 63 D63A  5 ± 2 26 ± 1  64 ± 23 64 E64A 208 ± 5  16 ± 1 43 ± 5  64.7 D63A, E64A, E67A 73 ± 9  780 ± 120 24 ± 4 65 E64N, L66S 153 ± 11980 ± 5   82 ± 12 67 E67A 16 ± 1  8 ± 1  52 ± 19 WT VEGF (CHO cell) 28 ±1 19 ± 1 16 ± 8 WT VEGF (293 cell) 30 ± 4 22 ± 2  28 ± 10   72.5 E72A,E73A 33 ± 1 30 ± 2  46 ± 12 75 N75A  23 ± 17 22 ± 1 11 ± 2 82 R82A 32 ±3 20 ± 1 38 ± 9 83 RIK(82-84)NLS >100000 29 ± 5 >2000 84 K84A 167 ± 6 24 ± 3 54 ± 5 84 R82A, K84A, H86A  >10000 48 ± 3  520 ± 150 86 H86A 53 ±1 15 ± 1  43 ± 13   91.5 H90A, E93A 34 ± 1 26 ± 1 33 ± 8 100  H99A,K101A 34 ± 5 30 ± 3 33 ± 1 103  E103A 61 ± 4 17 ± 1 33 ± 6 105  R105A 42± 5 38 ± 1  84 ± 34  107.5 K107A, K108A 78 ± 7 66 ± 3 25 ± 6  108.5KKDR(107- 77 ± 4 54 ± 5 26 ± 3 110)AAAA  109.5 D109A, R110A 30 ± 3 35 ±1 20 ± 1 113  R112A, E114A 40 ± 2 13 ± 2 29 ± 5 WT VEGF (CHO cell) 28 ±1 19 ± 1 16 ± 8 WT VEGF (293 cell) 30 ± 4 22 ± 2  28 ± 10¹The values for IC50 in the KDR-IgG and FLT-IgG binding studies are inthe absence of heparin (15 μg/ml). Errors associated with these valuesare ± S.E.M.²Mean residue number indicates the average position of the mutation(s).³Boldface sequence indicates mutations that potentially alter VEGFglycosylation.

It will be understood that one skilled in the art following the abovedetails concerning the preparation of several mutants hereof can prepareyet other mutations to the VEGF molecule in accordance with the generalparameters of the present invention as set forth in more detail supra.Attention is directed to FIGS. 16 to 18 where data on biologicalactivities for a number of variants is provided.

Comparison of VEGF, PLGF and PDGF Sequences—Plasmin catalyses thecleavage of the carboxy-terminal, heparin-binding region (111-165)releasing the VEGF₁₁₀ dimer which displays bioactivity in theendothelial cell growth assay and in the Miles permeability assay [Houcket al., J.

Biol. Chem. 267, 26031-26037 (1992)]. As such, we compared the sequenceof the receptor binding region of VEGF (ie. 1-110) with sequences ofhomologous proteins, PLGF, PDGFa and PDGFb. The sequences were alignedwith respect to the eight cysteines shared by this family of proteins.Six cysteines form intra-chain disulfides and two cysteines areinter-chain covalent linkages between monomers according to the homologywith PDGFb [Haniu et al., Biochemistry 32, 2431-2437 (1993) and Pötgenset al., J. Biol. Chem. 269, 32879-32885 (1994)]. Two short gaps,inserted in the VEGF and PLGF sequences, are located at the apex ofexternal loops based on the crystal structure of PDGFb dimer [Oefner etal., The EMBO J. 11, 3921-3926 (1992)]. VEGF₁₁₀ shares 47%, 15%, and 19%sequence identity and 63%, 24%, and 28% similarity with PLGF, PDGFa andPDGFb, respectively [George et al., Meth. Enzymol. 183, 333-351 (1990)].Inspection of sequence similarity and 25 divergence among these growthfactors offers little insight as to the specific epitopes that mediateVEGF receptor binding. Functional mapping of VEGF was conducted bysite-directed mutagenesis.

Clustered charged-to-alanine scan mutagenesis—Thirty mutants of VEGF₁₆₅were constructed by site-directed mutagenesis where groups of betweenone and four neighboring charged amino acids (Arg, Lys, His, Asp, andGlu) were replaced with alanind (Table 6). Plasmid DNA encoding thesemutants was transiently transfected in human 293 kidney cells and theamount of VEGF in the conditioned cell media was determined using twoVEGF-specific immunochemical assays. In FIG. 19 the results of apolyclonal/monoclonal ELISA are compared to those obtained with a dualmonoclonal assay. In the poly-/monoclonal assay, affinity purifiedpolyclonal antibody reacted with multiple epitopes while the monoclonalantibody 5F8 is specific for determinants in the carboxy terminal,heparin-binding region (111-165) of VEGF. In contrast, the dualmonoclonal ELISA utilized neutralizing and non-neutralizing monoclonalantibodies (Mabs A4.6.1 and 5F8, respectively). The use of twoimmunochemical detection methods assisted in the accurate determinationof mutant VEGF concentration in conditioned cell media. For most VEGFmutants, the results of two immunochemical analyses were in goodagreement, with transient expression levels ranging from 0.2 to 2 μg/mlof VEGF antigen in the conditioned media. Nearly all VEGF mutants wereexpressed with variable yield for repetitive transfections, with thenotable exception of the R56A mutant of VEGF. No immunopositive proteinwas detected with the R56A mutation despite re-construction of thevariant and numerous transfection attempts. It is interesting to notethat arginine is strictly conserved at position 56 in VEGF, PLGF andPDGF, suggesting that this amino acid plays a vital role in structuralintegrity and/or native protein folding. Significantly, mutations in theregion 82 to 86 were consistently underquantitated in the dualmonoclonal ELISA compared to those results obtained with thepoly-/monoclonal assay, indicating that the epitope recognized by theneutralizing monoclonal antibody, A4.6.1, includes this determinant inVEGF. The single amino acid substitution, R82A yields a mutant of VEGFexhibiting almost complete loss of immunochemical reactivity with MabA4.6.1 (FIG. 19). Furthermore, VEGF mutations H9OA, E93A displayed apartial loss of reactivity with Mab A4.6.1. These data suggest that theepitope of a neutralizing monoclonal antibody is localized to a regionof VEGF including amino acids 82 to 93.

Non-Reducing, SDS-PAGE Analysis of VEGF Mutants—A representative set oftransiently transfected supernatants (from 293 cells) containingapproximately 10 to 20 ng of VEGF or VEGF mutant were analyzed bynon-reducing SDS-PAGE. The gels were transferred and blotted asdescribed above using a panel of 5 murine monoclonal anti-human VEGF₁₆₅antibodies. Autoradiography of the immunoblots indicated a major band at45 kDa for wildtype and mutant forms of VEGF. This immunopositiveprotein band co-migrated with purified, dimeric VEGF₁₆₅ derived from CHOcells. For some mutants of VEGF, and for 293 cell-derived wildtype VEGF(but not VEGF derived from CHO cells), there appeared an additionalminor band at approximately 70 kDa. Apparent molecular weights for allalanine scan VEGF mutants, as indicated by SDS-PAGE, were equivalent tothat observed for wildtype VEGF₁₆₅ derived from 293 or CHO cells. Therewas no indication of degraded forms of VEGF that would yield lowermolecular weight species as has been observed for plasmin cleavage ofVEGF [Houck et al., J. Biol. Chem. 267, 26031-26037 (1992) and Keyt etal., The VIIIth International Symposium on the Biology of VascularCells; Heidelberg, Germany, p. 48 (1994)].

VEGF Binding to KDR Receptor is Primarily Mediated by R82, K84, andH86—The binding of VEGF mutants to soluble KDR-IgG was evaluated bycompetitive displacement Of ¹²⁵I labeled VEGF₁₆₅ in the absence orpresence of heparin. The list of mutations is given in Table 6. Inaddition to the specific amino acid substitutions, the table indicatesthe mean residue number for the position of the mutation(s). For a givenmutant, this number is the average of the altered positions. The resultsfor 27 charged-to-alanine scan mutants of VEGF in studies of binding toKDR-IgG are shown in FIG. 6, plotted with respect to the position of themutation(s). Wildtype VEGF₁₆₅ expressed in 293 cells and CHO cells wereequivalent with respect to displacement of ¹²⁵I labeled VEGF₁₆₅ in KDRbinding. The concentrations required to achieve half-maximal inhibition(IC₅₀) were 31 pM and 29 pM for 293- or CHO-derived VEGF₁₆₅,respectively (n=8 replicates each). The IC₅₀ values for wildtype VEGFwere not significantly different in the absence versus the presence of15 μg/ml heparin.

Many of the mutant proteins exhibited binding comparable to wildtypeVEGF. In fact, the binding to KDR for 19 out of 25 alanine scan mutantswas similar to that of wildtype VEGF; the average IC₅₀ for mutants withwildtype-phenotype was 29±18 pM (n=19). However, the most significanteffect on binding was observed with the R82A, K84A, H86A mutant of VEGFwhich exhibited 1000 fold decreased affinity for the KDR receptor in theabsence of heparin, relative to that of wildtype VEGF (FIG. 6).Interestingly, in the presence of heparin the binding of this triplemutant was only 10 fold decreased compared to that of wildtype VEGF.These results are consistent with VEGF binding to KDR as a function oftwo sites of interaction, a heparin-independent site in the 1-110 dimerand a heparin dependent binding site in the 111-165 domain. In theabsence of heparin, the binding of VEGF₁₆₅ to KDR is mediated entirelyby the 1-110 region. Without heparin, the mutations at 82, 84 and 86severely compromise the binding of VEGF to KDR. To evaluate the relativecontribution of the individual residues, single amino acid substitutionmutants of VEGF were constructed. The single mutations, R82A, K84A andH86A were found to display more modest decreases with respect to KDRbinding in the absence of heparin (FIG. 10). R82A VEGF exhibitedwildtype KDR binding, while K84A VEGF and H86A VEGF were approximately5.5 fold and 2 fold decreased in binding compared to that of wildtypeVEGF, respectively. All of the single alanine replacement mutants hadnormal binding affinity in the presence of heparin. While the 84position of VEGF was most dominant in the triple alanine mutant, thecombination of mutations at 82, 84 and 86 clearly exhibited asynergistic effect on the interaction with the KDR receptor.

In addition to the major KDR binding determinant, a minor site wasobserved in the 63 to 67 region. The triple mutant, D63A, E64A, E67AVEGF, was 3 fold reduced in binding to KDR in both the presence andabsence of heparin. Single amino acid mutations in this region displayeddifferent characteristics. Wildtype-like binding to KDR was observed forD63A VEGF and E67A VEGF. In contrast, E64A VEGF had 8 fold and 3 folddecreased binding in the absence and presence of heparin, respectively.Although modest in comparison to the major effects observed with R82A,K84A, H86 VEGF, the most potent effects with single alanine replacementof charged amino acids were observed for E64A VEGF and K84A VEGF.

VEGF Binding to FLT-1 Receptor Involves Interaction with D63, E64,and.E67 As was observed for KDR binding, most of the alanine scanmutants of VEGF bound FLT-1 with similar affinity as wildtype VEGF (FIG.7). Compared to KDR, there appeared less effect of heparin on the FLT-1binding of wildtype VEGF or the majority of mutants which displayedwildtype-phenotypic binding to FLT-1. The IC₅₀ values for wildtype VEGFwere 22±8 and 15±8 pM in the absence and presence of heparin,respectively (n=13). Analysis of alanine scan VEGF mutants indicated twosites of interaction with FLT-1 that co-localized with the KDR bindingdeterminants. A major site for FLT-1 binding involves the 63 to 67region of VEGF as indicated by the approximately 30 fold reduction inaffinity with D63A, E64A, E67A VEGF in the absence of heparin. This isin contrast to the results with KDR which indicated mutations in the63-67 region of VEGF exhibited only modest effects on KDR binding. Inthe presence of heparin, D63A, E64A, E67A VEGF binding to FLT-1 wasdecreased about 20 fold compared to wildtype VEGF. The major site of KDRinteraction (82-86 region) yielded only minor effects with respect toFLT-1 binding. R82A, K84A, H86A VEGF was slightly reduced in binding toFLT-1 in the presence or absence of heparin. Additional mutational sitesat the carboxy terminus were associated with minor effects on FLT-1binding. Interestingly, the major site mediating KDR interaction, thatwas localized to 82 to 86 region of VEGF, exhibited only a modest effecton FLT-1 binding. In contrast, the major site for FLT-1 binding waslocalized to the 63-67 region of VEGF, which displayed minor effects onKDR binding. The relative roles of major and minor receptor bindingsites are reversed for FLT-1 in comparison to that for KDR.

The Effect of Glycosylation on Receptor Binding—We altered theglycosylation sites of VEGF to confirm and extend the results observedwith alanine scanning mutagenesis. First, the role of a single putativesite of N-linked glycosylation at position 75 was evaluated for VEGF. Anunglycosylated form of VEGF was constructed, expressed in 293 cells andvisualized by SDS-PAGE and immunoblotting (FIG. 20). This mutant, N75AVEGF, appeared to have a lower molecular weight consistent with the lackof glycosylation at position 75, and by inference, this result confirmsthat wildtype VEGF expressed in 293 cells does contain N-linkedcarbohydrate at that site. The binding of N75A VEGF wasindistinguishable from that of wildtype VEGF for both KDR and FLT-1soluble receptors in the presence and absence of heparin. For thewildtype protein, N-linked carbohydrate at Asn⁷⁵ does not appear to playa role in mediating VEGF receptor binding.

Potential neo-glycosylation sites were inserted at three novel sites inVEGF to observe the effects of carbohydrate addition at or near theputative site of receptor binding. Surface accessible sites wereconsidered optimal in exterior loops or turns as predicted on the basisof the crystal structure of PDGFb dimer [Oefner et al., The EMBO J. 11,3921-3926 (1992)]. One such site (42-44 region) was selected as acontrol since no receptor binding determinants were identified in thisregion by charged-to-alanine scanning mutagenesis. The neocarbohydratesite in E42N, E44S VEGF was apparently glycosylated as indicated by theincreased molecular weight observed on SDS-PAGE immunoblots (FIG. 20).The N-linked carbohydrate at position 42 did not interfere with bindingto KDR or FLT-1 receptors as indicated by IC₅₀ values of 15 pM and 13pM, respectively.

Potential Glycosylation Site at Position 82 Results in SeverelyDecreased KDR Binding—Mutations of VEGF in the KDR binding siteintroduced a novel potential N-linked glycosylation site at position 82.RIK(82-84)NLS VEGF was constructed, expressed in 293 cells and evaluatedby SDS-PAGE immunoblotting (FIG. 20). The extent of additionalglycosylation at Asn82 was not apparent on the immunoblot forRIK(82-84)NLS VEGF as compared to the change in electrophoretic mobilityobserved with E42N, E44S VEGF. Although the RIK(82-84)NLS mutation hadlittle effect on apparent molecular weight, the effect on KDR bindingwas quite significant. RIK(82-84)NLS VEGF exhibited only partialdisplacement of the labeled VEGF in KDR binding assays in the absence ofheparin (FIG. 9A). The half-maximal inhibitory concentration forRIK(82-84)NLS VEGF was estimated to be 10,000 fold greater than thatobserved for wildtype VEGF. This mutant which exhibited virtually noaffinity for soluble KDR in the absence of heparin, was capable of fulldisplacement of VEGF in the presence of heparin, albeit at higherconcentrations. The relative affinity of RIK(82-84)NLS VEGF for KDR was50 fold decreased compared to that of wildtype VEGF with 15 μg/mlheparin. Interestingly, this putative extra-glycosylation mutationresulted in a mutant exhibiting normal affinity for FLT-1 (FIG. 9B).RIK(82-84)NLS VEGF and wildtype VEGF displayed similar FLT-1 bindingaffinity in the presence and absence of heparin. Mutations in the 82 to86 region (R82A, K84A, H86A and RIK(82-84)NLS) confer significantlydecreased interaction with KDR and normal binding to FLT-1. As such,RIK(82-84)NLS VEGF is a highly FLT-1 selective variant of VEGF.

Extra-glycosylation Site Mutant at Position 64 Decreases FLT-1, but notKDR Binding—A VEGF mutant was designed to introduce a neo-glycosylationsite in the region (63-67) which has been shown to mediate FLT-1binding. E64N, L66S VEGF was constructed, expressed in 293 cells andevaluated by immunoblotting for evidence of glycosylation. E64N, L66SVEGF was observed as a faint band with apparent increased molecularweight on SDS-PAGE (FIG. 20). The binding studies indicated that E64N,L66S VEGF was 40 fold reduced in FLT-1 binding in the absence of heparin(FIG. 9B). In contrast to the results observed with KDR-specificmutations in the 82-86 region, the putative extra-glycosylation mutant(E64N, L66S VEGF) displayed similar FLT-1 binding affinity as the triplemutant of VEGF (D63A, E64A, E67A). As with the corresponding triplemutant, E64N, L66S VEGF exhibited little change in the binding to FLT-1depending on the presence versus the absence of heparin (IC₅₀: 650 pMversus 980 pM, respectively). The mutants having FLT-1 specific effectsexhibited modestly decreased binding with KDR receptor. The relativebinding of D63A, E64A, E67A VEGF and E64N, L66S VEGF to soluble KDR wasapproximately 3 fold and 6 fold decreased, respectively. The mutationsin the 63-67 region of VEGF confer KDR selectivity in that these mutantsbind KDR similar to wildtype VEGF, but FLT-1 binding is decreased.

VEGF Mutants with Decreased KDR Receptor Binding are Weak EndothelialCell Mitogens—Mitogenic activities of VEGF and mutants of VEGF weredetermined using bovine adrenal cortical capillary endothelial cells.Wildtype VEGF, derived from 293 cells or CHO cells, induced half maximalproliferation at 28±10 pM (n=6) and 16±8 pM (n=9), respectively.Conditioned cell media from mock transfected 293 cells did not induceendothelial cell proliferation. The half-maximally effectiveconcentrations (EC₅₀) for most of the VEGF mutants were similar to thoseobserved for wildtype VEGF (FIG. 21). The most significant effect onendothelial cell proliferation was observed with mutations in the 82-86region. The EC₅₀ of R82A, K84A, H86A VEGF increased to 520±150 pM (n=4)such that mitogenic potency of this mutant was decreased to 5% ofwildtype VEGF. To confirm and extend this observation, theneo-glycosylation site mutant was also evaluated for its relativemitogenic potency. Induction of proliferation by RIK(82-84)NLS VEGF wasreduced to such an extent that wildtype-VEGF level growth was notachieved at the highest concentration tested (FIG. 11). Toquantitatively assess the potency of RIK(82-84)NLS VEGF, we compared theconcentration of the mutant required to achieve 20% of maximalVEGF-induced stimulation. The difference in EC₂₀ values for wildtypeVEGF and RIK(82-84)NLS VEGF (4 pM versus 230 pM, respectively) indicated60 fold reduced potency for the mutant with a neo-glycosylation site inthe region specific for KDR binding. The effect of these mutations onendothelial cell growth is consistent with the KDR binding data. Theaffinity of R82A, K84A, H86A VEGF and RIK(82-84)NLS VEGF with solubleKDR (in the presence of heparin) was reduced 10 fold and 50 fold,respectively, compared to that observed with wildtype VEGF. Sinceendothelial cells in vitro express surface and matrix associated heparinsulfates [Barzu et al., Biochim. Biophys. Acta. 845, 196-203 (1985)], itis appropriate to compare the mitogenic response of endothelial cells toVEGF or VEGF mutants with the binding data for those proteins to solubleVEGF receptors in the presence of heparin. Taken together, themutational analysis of VEGF by alanine scanning and extra-glycosylationprovide strong evidence that binding to KDR receptors on endothelialcells is a triggering event for the induction of proliferation observedwith VEGF.

VEGF Mutants with Decreased FLT-I Receptor Binding are Fully ActiveEndothelial Cell Mitogens—Alanine scan substitutions in the 63-67 regionof VEGF were shown to have normal binding to KDR and decreased bindingto FLT-1 (FIGS. 6 and 9). Triple and single alanine mutants (D63A, E64A,E67A VEGF, D63A VEGF, E64A VEGF, and E67A VEGF) were evaluated forinduction of endothelial cell growth. All of these mutants exhibitedmitogenic potency similar to that of wildtype VEGF (FIGS. 21 and 11).The mutant with a putative extra-glycosylation site in the 63-67 region;E64N, L66S VEGF also exhibited normal activity on endothelial cells(FIG. 21). These data reinforce the observation that FLT-1 deficientmutants of VEGF induce endothelial cell proliferation similar towildtype VEGF. Furthermore, these data suggest that VEGF binding toFLT-1 receptors on endothelial cells is unrelated to mitogenesis andproliferation. This mutational analysis has identified VEGF variantsthat are relatively selective for KDR or FLT-1 receptors. The data inthis report suggests an electrostatic component of VEGF:receptorinteraction, such that the determinants for KDR and FLT-1 includepredominantly positive or negatively charged regions of VEGF,respectively.

Concluding Remarks:

The foregoing description details specific methods which can be employedto practice the present invention. Having detailed such specificmethods, those skilled in the art will well enough know how to devisealternative reliable methods at arriving at the same information inusing the fruits of the present invention. Thus, however detailed theforegoing may appear in text, it should not be construed as limiting theoverall scope thereof; rather, the ambit of the present invention is tobe determined only by the lawful construction of the appended claims.All documents cited herein are hereby expressly incorporated byreference.

1. An isolated nucleic acid sequence comprising a sequence that encodesa vascular endothelial cell growth factor (VEGF) variant wherein saidvariant comprises mutations in the Kinase domain region (KDR) and/or theFMS-like Tyrosine Kinase region (FLT-1).
 2. The DNA sequence accordingto claim 1 wherein said variant contains mutations in the FLT-1 regioncomprising amino acids about 60 to
 70. 3. The DNA sequence according toclaim 1 wherein said variant contains mutations in the KDR regioncomprising amino acids about 78 to
 95. 4. The DNA sequence according toclaim 1 wherein amino acids 63, 64 and 67 are modified and/or aminoacids 82, 84 and 86 are modified.
 5. The DNA sequence according to claim1 encoding a vascular endothelial cell growth factor variant having thefollowing modifications: D63A, E64A, E67A, and/or R82A, K84A, H86A.
 6. Apolypeptide which comprises a vascular endothelial cell growth factorvariant containing a modification in the Kinase domain region (KDR)and/or FMS-like Tyrosine-Kinase region (FLT-1) such that the bindingcharacteristic of said region(s) is modified with respect to itsrespective receptor.
 7. The polypeptide according to claim 6 whereinsaid variant contains amino acid changes in the region comprising aminoacids 60 to
 70. 8. The polypeptide according to claim 6 wherein saidvariant contains amino acid changes in the region comprising amino acids78 to
 95. 9. The polypeptide according to claim 6 wherein amino acids63, 64 and 67 are modified and/or amino acids 82, 84 and 86 aremodified.
 10. The polypeptide according to claim 6 having the followingmodifications: D63A, E64A, E67A, and/or R82A, K84A, H86A.
 11. Apolypeptide according to claim 6 containing further amino acidmodifications that do not otherwise affect the essential biologicalcharacteristics.
 12. A replicable expression vector capable in atransformant host cell of expressing the DNA sequence of claim
 1. 13.Host cells transformed with the vector according to claim
 12. 14. Hostcells according to claim 13 which are Chinese hamster ovary cells.
 15. Acomposition of matter comprising the VEGF variant according to claim 6compounded with a pharmaceutically acceptable carrier.
 16. A method oftreatment which comprises administering a composition according to claim15.
 17. An assay for identifying candidates having agonistic orantagonistic properties with respect to KDR and/or FLT receptor binding,comprising contacting said candidates with a polypeptide according toclaim 6 and measuring the affect said candidate has on the bindingcharacteristics of said polypeptide to said KDR and/or FLT-1 receptors.